Defense Grid, because you like plants vs zombies
SPAZ, very fun game, hard to explain, 2d arcade space shooter with a galaxy map and very indepth upgrades and ship customization
Gratuitous Space Battles, If you like chess type games or watching space battles
Endless Space, freaking awesome 4x (space civ) game
Torchlight 2, is this considered indy? Great d2 style game
Some more tower defense games : Dungeon Defenders, Cubemen (freakin hard), Orcs Must Die, Sol Survivor (bleh graphics but fun game)
Recettear, anime style game dealing with running a item shop, selling to customers, and zelda like 2d dungeons
Evil Genius, I don't think this is technically indy but is basicly Dungeon Keeper...for james bond villans
Nexus, the juptier incident, it's sort of like homeworld but without building ships and much more focused on controling very indepth aspects of a few ships.
Flotilla, it's a rogue like for space combat sims, very interesting art style...fun, bit of a learning curve
From Dust, god game civ that looks amazing, really this is indie?
Uplink, a puzzle game where you are a hacker, it's done how you really would, running files and stuff, it's about timing and resource management
Magicka, umm...hard to explain, dungeon crawler that deals with mixing types of magic to do various spells, great humor
Star Ruler, a indie 4x, not as graphicaly pleasing as Endless Space and much diffrent playstyle
X3 Albion Prelude, I think the X games are indy? Basicly freelancer but less polished graphicly and with WAY WAY more indepth control on the systems, building bases and so on
They Bleed Pixles, sort of like super meat boy but with a lovecraft feel to it, some neat gameplay elements too