Suggestion for categories:
Aquaria (Bit Blot, Website) = Adventure
The Binding of Isaac = Rouge-like / Action
Blocks That Matter (Swing Swing Submarine, Indievania) = Puzzler - Platformer
Braid (Jonathan Blow, Website) = Puzzler - Platformer
Cortex Commands (Data Realms, Website) = Strategy
Gish (Cryptic Sea, Chronic Logic) = Platformer
Minecraft (Notch, Website) = Adventure
The Misadventures of P.B. Winterbottom = Puzzler - Platformer
Orcs Must Die! (Robot Entertainment, Steam Store) = Action / Strategy
Osmos = Strategy???
Plants Vs. Zombies (PopCap games, Website) = Strategy (but as kavazovangel said, not really indie anymore)
Terraria (Re-Logic, Steam Store) = Adventure
Trine (Frozenbyte Games, Steam Store, GamersGate, Impulse, Direct2Drive) = Platformer
World of Goo (2D Boy, Website) = Puzzle
VVVVVV (Terry Cavanagh, Website) = Platformer
Suggestions for more games:
To the moon - Freebird games - RPG - Desura=
http://www.desura.com/games/to-the-moon, Website=
http://www.freebirdgames.com/
Cthulu saves the world / Breath of Death VIII - Zeboyd Games - RPG - Steam=
http://store.steampowered.com/sub/8848/, Gamersgate =
http://www.gamersgate.co.uk/DD-CSW/cthulhu-saves-the-world Dungeons of Dreadmore - Gaslamp Games - Action / Rougelike - Steam =
http://store.steampowered.com/app/98800/?snr=1_6_4__13, Desura =
http://www.desura.com/games/dungeons-of-dredmor Amnesia: The dark decent - Frictional Games - Survival Horror - Website=
http://www.amnesiagame.com/#main, (and also on every digital retailer...)
Project Zombiod - The Indie Stone - Survival Horror / Action - Website=
http://projectzomboid.com/blog/,
http://www.desura.com/games/project-zomboid. Still in alpha stage