Every now and then I actually try to post something useful so that the bookmark to my own blog has some use beyond giving me the option to instantly vent on whatever is bothering me at the time.
To this end I have spent a little time mapping out what instances give rep for what faction simply for reference purposes. I for one can never remember which faction requires what instances to be run.
The sources are various but in the end I was able to filch most things from wowwiki in combination with wowhead and a few others. So yes the list exists, probably in a 1000 different places but for my own searching pleasures it can now be found here as well.
Non-horde factions have been conveniently left out because... well... I am lazy and I don't have any alliance characters. Additionally I might've forgotten some factions because I am disorganized too.
Undercity, Orgrimmar, Thunder Bluff, Silvermoon, Darkspear Trolls
No instances to run for these I am afraid. You will however be able to do some repeatable turn in quests for most of these and a lot of quests in Azeroth will boost reputation for these factions.
Shattered Sun Offensive
Large amounts of dailies can give SSO rep. However all instances on the island of quel'danas give SSO rep as well.
Visit the coilfang reservoir. Any Coilfang instance will do just fine.
The consortium has quest hubs all over outland. The instance to go for rep is Mana Tombs.
Hellfire citadel instances will all give Thrallmar rep.
Lower city rep can be gained in Auchenai crypts, sethekk halls or shadow labyrinth. (terokkar).
Anything in Tempest keep will do for Sha'tar rep.
Faction rep can be gained in the black temple
Keepers of Time
Old Hillsbrad and Black morass are your friends if KoT faction is what you need.
Zul'Gurub is the place to gain faction rep.
Hand in scourgestones or kill mobs in the plaguelands for reputation gain with this faction. No instance runes available.
Aldor / Scryer
Each faction has turn in items to gain rep. There are no instance runs available. Slay demons or blood elves for the required turn in items.
Kill mobs around skettis and do the sha'tari quests. There is no instance to run to gain skyguard rep with.
No instance runs available for rep. Quests in Nagrand and whacking ogres / orcs should gain you some Mag'har rep.
Another faction you can't gain rep with through instances. There are however (daily) quests that will help with gaining Ogri'la reputation.
These chaps have a few repeatable quests. Most noteworthy is the collection of plants from the underbog instance which is repeatable.
The lunar festival quests and whacking twilight mobs in silithus will gain you CC rep. There are no instances to run.
Frostwolf Clan, Defilers, Warsong Outriders
These are PVP factions. If you want reputation for these your best bet is to run BattleGrounds. A lot of BGs. Frostwolf clan offers some extra quests and repeatable quests based in or around alterac valley.
Ratchet, Booty Bay, Gadgetzan, Everlook
Neutral factions that have banded together under the name steamwheedle cartel. There's no instance runs available for these. Go to the neutral cities and pick up quests to gain reputation. These factions are tied together, if you cause problems with one of them you will end up having issues with all of them.