1. Reputation Basics
Your reputation affects how monsters or creatures will interact with you. There are several reputation levels. These are taken directly from the World of Warcraft site.

Exalted - Highest level of accolade attainable with a faction
Revered - Special reputation level reserved for special heroes
Honored - 10% discount on bought items from vendors
Friendly - Standard reputation level for factions on a players team
Neutral - Standard reputation level for factions not on a players team that are not KOS
Unfriendly - Cannot buy, sell, or interact
Hostile – KOS
Hated - KOS; all opposing team factions are set permanently to the lowest level here

At Exalted, you can also purchase a mount from that faction, if that faction is actually on your team. If you are Exalted with Gadgetzan, for example, there is no mount from them.

Only Gnomes and Dwarves may ride Mechanostriders.

Tauren may only ride Kodo Beasts. In 1.8.0, it is planned for them to be able to ride Wolves.

With patch 1.8.0, you may now move your cursor over the reputation bar to view the amount that you have. Pretty nifty.


2. Avalible Factions
I have listed here all the avalible factions that are currently implemented. Note that though they exist, you may not be able to interact with them.

Alliance

Darnassus
Gnomeregan Exiles
Ironforge
Stormwind

Alliance Forces

League of Arathor
Stormpike Guard
Silverwing Sentinels

Horde

Darkspear Trolls
Orgrimmar
Thunder Bluff
Undercity

Horde Forces

Frostwolf Clan
The Defilers
Warsong Raiders

Steamwheedle Cartel

Booty Bay
Everlook
Gadgetzan
Ratchet

Other

Argent Dawn
Bloodsail Buccaneers
Brood of Nozdormu
Cenarion Circle
Gelkis Clan Centaur
Hydraxian Waterlords
Magram Clan Centaur
Ravenholdt
Revantusk Village
Shen’dralar
Syndicate
Thorium Brotherhood
Timbermaw Furbolgs
Wildhammer Clan
Wintersaber Trainers


3. Battleground Factions
The Battleground Factions are factions specific to each battleground. Each battleground contains 1 Faction per side.

Arathi Basic: League of Arathor - Alliance/The Defilers - Horde
Alterac Valley: Stormpike Guard - Alliance/Frostwolf Clan - Horde
Warsong Gulch: Silverwing Sentinels - Alliance/Warsong Raiders - Horde

The rewards offered by the Battleground Factions can be found all at Blizzard's official website. However, I am here to give you some statistical information that they do not.

Arathi Basin: Every 330 resources you/your team gathers, you gain 10 Reputation with your faction. Everytime you win, you get a 3 Marks of Honor, which you may turn in for 50 Reputation. The first turn in of these Marks of Honor should grant 800 Reputation. If you lose, you only gain 1 Mark of Honor.

Essentially, this equals to hundreds of games that need to be played, and won, to even get close to Exalted.

Alterac Valley: Everytime you or an ally turns in items, whether this be Blood or Flesh or Medals, it will grant everybody on your team, in the game, 1 Reputation point. Some certain turn ins will grant everyone 2 Reputation points. I believe that the specific race player item turn ins only grant you the Reputation bonus, but I could be wrong here.

Slaying an enemy Captain gives 100 Reputation. Slaying an enemy NPC gives 5 Reputation. Winning the game grants 350 Reputation. The 350 could be off...

Warsong Gulch: Having not played this for a long time, I will not yet update this until I have more information.


4. The Steamwheedle Cartel
To be implemented soon.


5. Argent Dawn
The Argent Dawn is a faction of warriors dedicated to eradicating the Scourge from Lordaeron. With much of their manpower based in the Western and Eastern Plaguelands, the Argent Dawn constantly strives to defeat their Undead foes to the arctic north.

All players start at 0/3000 Neutral with Argent Dawn.

Ways to increase Argent Dawn Faction:

Do Argent Dawn Quests
Slay Undead in the Plaguelands
Slay Undead in Stratholme
Slay Undead in Scholomance
Use Valor Tokens
Do Caludron Quests

The Undead in the Plaguelands will each increase your reputation with Argent Dawn by 5 for each kill. The max they can bring you up to is 3000/6000 Friendly.

The Undead in Stratholme/Scholomance will each increase your reputation with Argent Dawn by 5 for each kill. The max they can bring you is 6000/12000 Honored.

The Undead Bosses in Stratholme/Scholomance will each increase your reputation with Argent Dawn by 25 for each kill. The max they can bring you is 10500/21000 Revered.

Using Valor Tokens will each increase your reputation with Argent Dawn by 25. To get Valor Tokens, you must either turn in 20 Minion's Scourgestones, 10 Invader's Scourgestones, or 1 Corrupter's Scourgestone.

When you have a Commission from Argent Dawn, each Undead you slay in the Plaguelands/Stratholme/Scholomance has a chance to drop a Scourgestone. All Undead around and below Level 56 will drop Minion's Scourgestones. All Undead above Level 56 and all elite Undead will drop Invader's Scourgestones. All Undead bosses will drop Corrupter's Scourgestones.

Turning these in will each net you 1 Valor Token. I recommend getting up to at least halfway past Honored before using your Valor Tokens.

The Cauldron Quests require you to bring different ingredients to a Cauldron, dumping them in, and thus, gaining faction with Argent Dawn. At level 60, Felstone Field only grants 15 Reputation Points, compared to the 25 of each of the other 3 farms. To gain the required ingredients for doing the Cauldron quests, you must have in your possession the Vitreous Focuser to gather the required reagents. The collectable reagents are:

Osseous Agitator: Undead from Felstone's
Somatic Intensifier: Undead from Felstone, Dalson's, and Writhing's
Ectoplasmic Resonator: Undead from Gahrron's

Additionally, you must purchase 1 Arcane Quickener each time you want to put the ingredients within the caludron. Each one takes up one inventory slot, so unless you clear your bags, you will be making a lot of runs back and forth.

Felstone Field: 1 Arcane Quickener, 4 Runecloth, 6 Osseous Agitator
Dalson's Tear: 1 Arcane Quickener, 4 Runecloth, 5 Somatic Intensifier
Writhing Haunt: 1 Arcane Quickener, 4 Runecloth, 5 Somatic Intensifier
Gahrron's Withering: 1 Arcane Quickener, 4 Runecloth, 4 Ectoplasmic Resonator

Rewards for Reputation with Argent Dawn:

Friendly
Enriched Mana Biscuts

Honored
Enriched Manna Biscuit
Recipe: Transmute Air to Fire (Alchemy)
Plans: Girdle of the Dawn (Blacksmithing)
Pattern: Dawn Treaders (Leatherworking)
Pattern: Argent Boots (Tailoring)
Formula: Powerful Anti-Venom (First Aid)
Formula: Enchant Bracer - Mana Regeneration (Enchanting)

Revered
Blessed Sunfruit
Blessed Sunfruit Juice
Major Healing Potion (Limited Supply: 4)
Major Mana Potion (Limited Supply: 4)
Plans: Gloves of the Dawn (Blacksmith)
Pattern: Argent Shoulders (Tailoring)
Pattern: Golden Mantle of the Dawn (Leatherworking)
Formula: Enchant Bracer - Healer (Enchanting)
Arcane Mantle of the Dawn (+5 Arcane Magic Resistance to Shoulders)
Shadow Mantle of the Dawn (+5 Shadow Magic Resistance to Shoulders)
Flame Mantle of the Dawn (+5 Fire Magic Resistance to Shoulders)
Frost Mantle of the Dawn (+5 Frost Magic Resistance to Shoulders)
Nature Mantle of the Dawn (+5 Nature Magic Resistance to Shoulders)

Exalted
Chromatic Mantle of the Dawn (+5 To All Magic Resistance to Shoulders)


6. Bloodsail Buccanneers
To be implemented soon.


7. Brood of Nozdormu
The Brood of Nozdormu, the Bronze Dragonflight. A majestic flight indeed. However, with the imminent threat of the Silithid, Anachronos must choose a champion amongst the mortal races to lead the fight against the ever-growing threat.

All players start at 0/36000 Hated with Brood of Nozdormu.

Ways to increase Brood of Nozdormu Faction:

Complete RRQ's
Slay monsters within Ahn'Qiraj

Currently, the only way to increase the Brood of Nozdormu reputation is by completing a long quest line. Starting in Cenarion Hold, you get a quest to slay the Broodlord Lashlayer within Blackwing Lair. He only drops his head once, so you must nominate one person to recieve it. You turn in the head, and you recieve a quest to collect 200 Silithid Carapace Fragments, which then grants you the Proxy of Nozdormu. When you "deputize" another player, they are allowed to collect Carapace Fragments for you, and you in turn will give them to gain reputation with the Brood of Nozdormu. Last I heard, the number was 42000.

At Neutral, you may begin the quest line from Anachronos to open the gates of Ahn'Qiraj, and you will be granted a ring.

It is said that once the gates open, reputation will be much easier to gain, as each monster slain grants 100-200 Reputation. However, I cannot confirm this as the server I play on (Gurubashi) has yet to open the gates!


8. Cenarion Circle
To be implemented soon.


9. The Centaur Clans
Many consider the Gelkis Centaur to be the "good" ones and the Magram to be the "bad" ones. But it doesn't really matter which clan you ally yourself with.

To ally with a clan, you must kill the opposing clan's members until you reach the Friendly level. Once there, you may recieve quests from either Uthek the Wise or Warug, for Gelkis and Magram, respectively.

There seems to be no other way to improve your standings with them, including doing their own quests! The quests themselves are quite easy, and seem to just be there to offer some extra experience from questing. There seem to be no buyable rewards for doing this, but some may be implemented later. This is still highly doubtful.

If you are trying to maximize reputation between your normal factions, I would reccommend not even speaking with these Centaur Clans. It grants some reputation-less XP, so it is better to skip them altogether.


10. Ravenholdt Manor
To be implemented soon.


11. War in the Hinterlands
Within the Hinterlands lies two warring factions: the Dwarven Wildhammer Clan and the Trolls of Revantusk Village. Based within Aerie Peak, the Wildhammer Clan has ties with the Alliance, while Revantusk Village is with the Horde.

Players may enter the Hinterlands from the Hillsbrad Foothills, in the northeast corner, near the Thoradin Wall.

Entering from this location will place players almost directly within Aerie Peak, the Wildhammer Clan central. Horde players, beware of the Alliance and their Gryphon friends!

Revantusk Village is located on the far eastern coast, in the far south. Isolated and difficult to reach, all Alliance players should beware of Horde from this location.

To increase reputation with the Wildhammer Clan, any Alliance player may complete their quests, slay Trolls within the Hinterlands, or turn in Troll Tribal Necklaces as an RRQ.

To increase reputation with Revantusk Village, any Horde player may complete their quests. Unfortunately, there seems to be no way to further increase Revantusk Village reputation beyond Neutral, due to a limited amount of quests.

As of 1.9.0, there is no reward for gaining Revered or Exalted faction levels with the Wildhammer Clan or Revantusk Village. It is noted that it may simply be impossible to even gain Friendly with Revantusk Village. The Wildhammer have one, albeit slow, RRQ, and this opens up unlimited faction points. Perhaps Revantusk Village will gain one soon?


12. Shen'dralar
The Shen'dralar is a group of Elves within the Dire Maul. Hiding within the Athenaeum, the Elves continue to siphon magic from the demon Immol'thar.

Currently, the Shen'dralar offer little for their reputation. Reputation is granted for completing the Mage Crystal Water quest and for turning in Librams/Books. There is a vendor for the Shen'dralar... so I guess Honored gives you a little discount. Otherwise, it seems the Shen'dralar currently offer nothing much of value.

There are rumors circulating that the Prince will reveal the location of the Ashbringer if you bring the Head of Nefarian, the Head of Broodlord, and be Revered with them. Then again, this will be near impossible.


13. Thorium Brotherhood
The Thorium Brotherhood is a group of renegade Darkiron Dwarves who would rather exploit the world than sit in their fortress all day long. Based in Thorium Point in the Searing Gorge, the Thorium Brotherhood specializes in blacksmithing, and creating some of the greatest and strongest items ever. However, their expertise also expands into the fine arts of Tailoring, Leatherworking, Alchemy, and Enchanting.

All players start at 0/3000 Neutral with the Thorium Brotherhood.

Ways to increase Thorium Brotherhood Faction:

Do Thorium Brotherhood Quests
Complete RRQ's

Thorium Point offers quite a few quests, all which may be completed for the best and max amount of reputation around level 48. Additionally, in Gadgetzan, Blacksmiths may take up the Imperial Plate quests. This requires a lot of Thorium Bars to turn in, and you should get around 1150 points of reputation with the Thorium Brotherhood.

To complete all 7 of them, you must bring at least 270 Thorium Bars. Turn them all in, and you get all the plans, plus lots of reputation bonus.

There are also quite a few RRQ's with the Thorium Brotherhood. The first, which is gained after completing the quest What the Flux?, is to create Fiery Flux. You may do this by gathering 2 Incendosaur Scales and 1 Coal, along with any of the following three:

4 Kingsblood
4 Iron Bar
10 Heavy Leather

Each turn-in grants 25 Reputation points, so prepare a lot in advance.

Once you reach Friendly with the Thorium Brotherhood, you recieve another RRQ known as Gaining Acceptance. Apparently, this Fiery Flux can be enhanced wit Dark Iron Residue. Bring about 1000 Dark Iron Residue, and turn it all in to Master Smith Burninate. You can only turn them in in groups of 4, so it takes a long while to do this. Dark Iron Residue is dropped by any mob within Blackrock Depths.

Once you reach Honored with the Thorium Brotherhood, you can only increase your reputation with them further by doing once of the following.

Favor Amongst the Brotherhood, Blood of the Mountain
Favor Amongst the Brotherhood, Core Leather
Favor Amongst the Brotherhood, Dark Iron Ore
Favor Amongst the Brotherhood, Fiery Core
Favor Amongst the Brotherhood, Lava Core

Dark Iron Ore - The most common way to improve standing. You must turn in 10 Dark Iron Ore for 50 Reputation Points. Many people buy the Dark Iron Ore, or a rather large guild will pool to one person to get them up to Exalted.
Core Leather - Turning in 2 Core Leather, skinned from the Ancient Core Hounds in Molten Core, grants 150 Reputation Points.
Blood of the Mountain, Fiery Core, Lava Core - All turn-ins grant 200 Reputation Points. Guilds that farm Molten Core often can use this to improve the standing of various guild members easily. It just takes time...

The best way for a guild to do this is to sell a Core, then use the money to buy Blood of the Mountain/Dark Iron Ore (whichever ends up being the cheapest) to give a person Revered. Easy as pie.

Rewards for Reputation with Thorium Brotherhood:

Friendly
Recipe: Transmute Elemental Fire (Alchemy)
Plans: Dark Iron Bracers (Armorsmithing)
Pattern: Flarecore Gloves (Tailoring)
Pattern: Molten Helm (Elemental Leatherworking)
Pattern: Corehound Boots (Tribal Leatherworking)
Formula: Enchant Weapon - Strength (Enchanting)

Honored
Plans: Dark Iron Reaver (Swordsmith)
Plans: Dark Iron Destroyer (Axesmith)
Plans: Fiery Chain Girdle (Armorsmith)
Plans: Dark Iron Helm (Armorsmith)
Pattern: Flarecore Mantle (Tailoring)
Pattern: Flarecore Robe (Tailoring)
Pattern: Black Dragonscale Boots (Dragonscale Leatherworking)
Formula: Enchant Weapon - Mighty Spirit (Enchanting)

Revered
Plans: Black Amnesty (Weaponsmith)
Plans: Blackfury (Weaponsmith)
Plans: Dark Iron Gauntlets (Armorsmith)
Plans: Fiery Chain Shoulders (Armorsmith)
Plans: Dark Iron Leggings (Armorsmith)
Pattern: Flarecore Leggings (Tailoring)
Plans: Molten Belt (Elemental Leatherworking)
Plans: Corehound Belt (Tribal Leatherworking)
Plans: Chromatic Gauntlets (Dragonscale Leatherworking)
Formula: Enchant Weapon - Mighty Intellect (Enchanting)

Exalted
Plans: Sulfuron Hammer (Blacksmith)
Plans: Nightfall (Axesmith)
Plans: Ebon Hand (Hammersmith)
Plans: Dark Iron Boots (Armorsmith)


14. Timbermaw Hold
The Timbermaw Furbolgs, taking residence in Felwood and Azshara, remain the only true and uncorrupted Tribe of their whole once-noble race. The Timbermaw control Timbermaw Hold, a large passageway between Felwood, Moonglade and Winterspring, and have a large hold over western Azshara. They have had time to create a few special items that they would gladly sell to their allies.

All players start at 2500/3000 Hostile with the Timbermaw Hold.

Ways to increase Timbermaw Hold Faction:

Slay Deadwood Furbolgs
Slay Winterfall Furbolgs
Complete Quests
Complete RRQ's

The Timbermaw Furbolgs initially start Hostile with you, meaning they will attack you. Slaying one will drastically decrease your chance of ever being Friendly with them. If you get to at least Unfriendly with them, you can walk through Timbermaw Hold without fear forever. Some people can just kill their way through each time, but I find that counter-productive. Besides, I could get some killer recipes, so why not?

Now, recently added in Patch 1.9.0, there are more ways to earn reputation for Timbermaw Hold. When you do the quests offered by Grazle, Nafian, or Salfa, you can then open up repeatable gathering quests. The Deadwood Furbolgs just outside Timbermaw Hold drop the Headdresses you can turn. It's 5 for 50 Reputation. Additionally, the Winterfall Furbolgs drop Beads you can collect for the same 5/50 reward. However, the old method of 75 rep repeatable quest has been taken out, so this collection quest is the only way to go.

Friendly
Recipe: Transmute Earth to Water (Alchemy)
Pattern: Warbear Harness (Tribal Leatherworking)
Pattern: Mooncloth Boots (Tailoring - Only avalible for completing the quest Sacred Cloth, which can be gained at Tailoring 290 and requires turning in 2 Mooncloth. Also rewards 100 points of Timbermaw Furbolg Reputation)

Honored
Plans: Heavy Timbermaw Belt (Blacksmithing)
Formula: Enchant Weapon (Enchanting)
Pattern: Might of the Timbermaw (Leatherworking)
Pattern: Warbear Woolies (Tribal Leatherworking)
Pattern: Wisdom of the Timbermaw (Tailoring)

Revered
Pattern: Timbermaw Brawlers (Leatherworking)
Pattern: Mantle of the Timbermaw (Tailoring)


15. Wintersaber Trainers
The Wintersaber Trainers offer, for the Alliance, extra mounts. Based in northern Winterspring, Rivern Frostwind will offer to sell you Wintersaber Mounts, which are Epic and move at 100% extra speed... provided you prove yourself an Exalted buyer. However, there is a drawback: you must also be Exalted with Darnassus to gain Tiger Riding. For those non-Night Elves, you have a long haul ahead of you...

All Alliance players start at 0/3000 Neutral with the Wintersaber Trainers.

Ways to increased Wintersaber Trainers Faction:

Complete RRQ's

There are 3 RRQ's with the Wintersaber Trainers. The first one, Frostsaber Provisions, requires 5 Shardtooth and 5 Chillwind Meat. They are quest items, so you cannot farm a bunch at once and turn them all in. PITA ain't it? Anyways, grab the meats, and return them for... 50 Reputation points. However, there is a light at the end of the Neutral tunnel.

At Friendly, you may choose to also do Winterfall Intrusion. This requires you to kill 5 Winterfall Shaman and 5 Winterfall Ursa. This is a two-fold grind for the Alliance; you can gain both Timermaw and Wintersaber Faction this way. Ride down to the village, slay the required Furbolgs, then ride back up. This is by far the easiest and best way to get Wintersaber Reputation, especially in a group.

At Honored, you may choose to also do Rampaging Giants. An elite quest that requires the slaying of 4 Frostmaul Giants and 4 Frostmaul Preservers, this quest is not worth the time involved compared to the other two above. You need to head to the far south of Winterspring, have a group to slay 8 of these powerful Giants, then ride all the way back up. For the same amount of Reputation as the previous two. I would reccommend just skipping this; it is too hard and long to be a viable way to get Reputation.

At Exalted, you are finally worthy enough to purchase a Winterspring Frostsaber! For a meager 800 Gold, you may finally have your own Frostsaber Tiger! This is TRUELY a mark of honor and recognition, either that you play WoW too much or you are truely a grand hero. I prefer the latter, but people mostly give you the former. Enjoy the mount!