The Best Indie Game You Have Ever Played.

Killing Floor.

Paranormal/Payday: The Heist/Terraria.

To the Moon, Penumbra series, Uplink and Superbrothers; Sword and Sworcery
Also games from Amanita Design like Machinarium and from Darkling rooms/Johnathan Boakes like the Darkfall Series and the Lost Crown

Minecraft

Shank 1/2

FTL and Sword of the Stars: The Pitt... I seem to love these almost never-ending rougelikes. Well, they're not never-ending, just really hard to beat.

1. Torchlight 2
2. The Binding of Isaac
3. Guacamelee! (Vita)

Can't really name just one. Super meat boy, isaac, sword of the stars, ftl, rogue legacy, bastion, spelunky. There are so many good ones.

BeamNG .drive

Aquaria

Kerbal Space Program

Shank

World of Goo

world of goo ;)
no, really

I don't really know what qualifies as indie nowadays but Terraria, Gnomoria, Minecraft, Revenge of the Titans, Defense Grid.

Dominions 3. The 4th will be out soon.

Along with

DWARF FORTRESS

and aurora ( pentarch )

iron and steam

histwar

Based on the hours I played it I'd have to say Guns of Icarus Online

Space Pirates and Zombies.

Psychonauts! :)

crimsonland

i have enjoyed torchlight 2 and super meat boy

Rogue Legacy

Limbo with no doubt.

Guncraft

Bastion, Interstellar marines, Nation red, Red orchestra/Rising storm, Torchlight 2

So far "Braid"

Binding of isaac.