Since I'd forgotten there was a guide forum, and the general thread is dead, I decided to move it here. Please don't post in the old anymore.
This is my compilation, as complete as I can personally make it, of all the ways to get rep with each faction. If I miss any, please post them. There may be errors, again, please post so I can fix them. RRQ= Repeatable Reputation Quest, for the unintiated.
*****Thrallmar / Honor Hold*****
These are your basic introductory factions, basically horde/alliance, in the outlands. They are named after the cities from which most of their quests come. Questing can easily bring you to Honored with them, then try the following:
-----Kills-----
Hellfire Citadel, Ramparts and Blood Furnace: to Honored
Hellfire Citadel, Shattered Halls: to Exalted
Hellfire Citadel, any Heroic: to Exalted
Fel Orc mobs in Hellfire Peninsula: to Friendly
-----Turnins/RRQs-----
Hellfire Fortifications (Daily) - 250 rep to Exalted
*****Cenarion Expedition*****
These druids from the Cenarion Circle have split off from the main organization, and have quest hubs at Veil Reskk in Blade's Edge and Cenarion Expedition in Zangarmarsh.
-----Kills-----
Coilfang Reservoir, Slave Pens and Underbog: to Honored
Coilfang Reservoir, Steam Vaults: to Exalted
Coilfang Reservoir, any Heroic: to Exalted
-----Turnins/RRQs-----
10x Unidentified Plant Parts from any mob in Zangarmarsh: 250 rep per turnin to Honored
1x Uncatalogued Species (occasionally gotten from the above turnin): 500 rep per turnin to Exalted
1x Coilfang Armament (Steamvaults trash drop): 75 rep per turnin to Exalted (250 first turnin)
*****Sporeggar******
Cute little mushroom men in Zangarmarsh. You start at Unfriendly with these, and reach neutral either by grinding Bog Lords or by doing the quests in the Spawning Glen of SE Zangarmarsh. At various repuation levels, they'll have quests for different locations, including a couple of Underbog quests with fun rewards.
-----Kills-----
Any Bog Giant: to Honored
Any Bog Strider: to Revered
-----Turnins/RRQs-----
Turn in 10 Pods from the Spawning Glen: 750 (I think) rep to Friendly
Turn in 10 Bog Lord Tendrils from any Bog Lord: 750 (I think) rep to Friendly
Turn in 10 Glowcap (gathered directly throughout the zone): 750 to Friendly
Turn in 10 Sanguine Hibiscus from the Underbog:750 rep to Exalted
Now that we're friends... (Naga-killing RRQ): 750 rep to Exalted
Turn in 10 Fertile Spores from various Zangarmarsh mobs: 750 rep to Exalted
*****The Scryers/The Aldor*****
These conflicting factions in Shattrath City start Neutral to everyone, and each player must pick a faction with which to align themselves via a quest from Khadgar in the Terrace of Light. Each has a section of Shattrath to themselves, and special 'inscriptions' (shoulder enchants). Note that any gain of reputation with one faction will reduce the other.
-----Kills-----
None.
-----Turnins/RRQs-----
Turn in 10 Marks of Kil'jaeden [Aldor] or 10 Firewing Signets [Scryer]: 250 rep to Honored
Turn in 1 Mark of Kil'jaeden [Aldor] or 1 Firewing Signet [Scryer]: 25 rep to Honored
Turn in 10 Marks of Sargeras [Aldor] or 10 Sunfury Signets [Scryer]: 250 rep to Exalted
Turn in 1 Mark of Sargeras [Aldor] or 1 Sunfury Signet [Scryer]: 25 rep to Exalted
Turn in 1 Fel Armament [Aldor] or 1 Arcane Tome [Scryer]: 350 rep to Exalted, see below
Marks of Kil'jaeden and Sargeras come from Burning Legion members of all types, wtih Fel Armaments a rare drop from the same. Firewing Signets and Sunfury Signets drop from Blood Elves in Outland, with Arcane Tomes a rare drop from them. The Armament and Tome turnins reward Holy Dust/Arcane Runes which are turned in for inscriptions at the factions' respective banks.
*****Lower City*****
Refugees in Shattrath, some quests from them can be found in the lower city itself.
-----Kills-----
Auchindoun, Sethekk Halls: to Honored
Auchindoun, Auchenai Crypts: to Honored
Auchindoun, Shadow Labs: to Exalted
Auchindoun, Heroic: to Exalted
-----Turnins/RRQs----
30x Arakkoa Feather: 250 rep to Honored
*****The Sha'tar*****
The Naaru of Shattrath, not a significant faction until Level 70. I could use more info on these. Small base in the southern Bone Wastes is the only faction-based zone known to me, other than Shattrath.
-----Kills-----
Any Tempest Keep instance, heroic or not: to Exalted