We could put one together ourselves. After a really quick run through TIGdb and my (very limited) memory, here are some possible nominees:
Best Action Game: Pro Killer Man, Destructivator, Samurai Railroad Mansion
Best Platformer: Iji, Rescue the Beagles
Best Shoot 'em Up: Ad Nauseum 2, Everyone Loves Active 2
Best RPG: Barkley, Shut up and Jam: Gaiden, Iffermoon
Best Adventure Game: Ben There, Dan That!, Little Girl in Underland, Nanobots
Best Strategy Game: Artifact's House Globe
Best Sim: ?
Best Fighting Game: Action DooM 2: Urban Brawl
Best FPS: Action DooM 2: Urban Brawl, 8bit Killer
Best Puzzle Game: Cursor*10, Fantastic Contraption, Karoshi 2, S.T.A.C.K.E.R.
Best Roguelike: Legerdemain, MageGuild, The Sewer Goblet
Best IF: Gun Mute [I don't know many IF games!]
Best Physics Game: Off-Road Velociraptor Safari
Best Browser Game: Dino Run, GINORMO SWORD, Qwop
Best Multiplayer Game: Cowboyana, Treasure Treasure
Best Remake: Quest for Glory II
Best Art Game: Aether, Execution, The Graveyard, Gravitation, I Wish I Were the Moon
Best Humor Game: Barkley, Shut up and Jam: Gaiden, Shit Game, Twin Hobo Rocket, You Have to Burn the Rope
Most Innovative: Seven Minutes, ROM CHECK FAIL, Colourblind, You Have to Burn the Rope
Most Challenging: Destructivator, FLaiL, Jumper 3, Mighty Jill Off
Best Graphics: ?
Best Audio: ?
Best Writing: ?
Damn, doing that just made me realize how many good indie games got released this year. I'm sure I left a bunch of great games out, too.
But yeah, anyway... if we agree on the nominees, we can do a series of polls.