Hard to limit it to just one so I'll say three:
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Do games that were released on consoles count? Eschatos is AMAZING and was made by a small indie team.
On Steam, probably Satazius or Exceed 2nd. Amazing shmups.
For non shmups, Bleed, They Bleed Pixels, and Rogue Legacy are amazing fun.
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Oh god world of goo is definitely one of my favorite indie games but I have played so many that it is hard to choose. Terraria was good, Monaco was good, bastion and the binding of Isaac were good. Just too many good choices.
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Antichamber
Thomas Was Alone
Plain Sight
Audiosurf
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That's hard to say actually... The winner for me is probably Minecraft.
Honorable mentions:
Amnesia - The Dark Descent
Braid
Cave Story
Don't Starve
FTL - Faster Than Light
Hotline Miami
Knytt Stories
Legend of Grimrock
Limbo
Little Inferno
Mount & Blade - Warband
Papers, Please
Slender - The Eight Pages
Spelunky
Surgeon Simulator 2013
Terraria
World of Goo
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Little Inferno. I don't know why but I really like it.
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To all those saying Game Dev Tycoon... You do realize that it was a complete shameless rip off of Kairosoft's game Game Dev Story, right? Fun, yes. But then again, so was the game they ripped off...
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The idea of Minecraft is not bad, but it's nothing new; beside that I cannot understand how can someone list a poor optimised sandbox game with no actual story, developed on a poor game engine with unappealing graphics, as the best indie game.
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