The Best Indie Game You Have Ever Played.

SpaceChem

There is no one best. There are many bestests!

Well, in my book anyway...

Psychonauts, Gunpoint, Limbo, Surgeon Simulator 2013, FTL, Proteus, Telltale's The Walking Dead, Monaco, Botanicula, Hotline Miami, The Swapper, Minecraft, FEZ...

Trine 2

Tie between Mark of the Ninja (I think that's indie...) and Hotline Miami

Skyrim

The Walking Dead and To The Moon :)

I'll probably date myself with this; but here goes: Chron X

The original and first ever online collectable card game.

Is Hack (now NetHack) indie enough? Haha. Too common? Mindwalker. It's in the running for first 16-bit game. Indie title for the Amiga over 20 years ago. I never beat it but if it got re-released on Steam... it would be on. And I think a lot of you would love it. It's way out in left field, but it makes sense... a little more sense than Fez at least. It's just weird. Used to be you couldn't find any evidence on YouTube, but finally somebody has a video up (and thankfully, with explanations—my father got it from a newsgroup, no instructions... took us a while to figure out what's what). Have a look.

But I suppose you mean newer ones. I was quite impressed with Thomas Was Alone, actually. Now Fez is kinda blowing my mind. I know a lot of people are mad at Phil Fish with some of his remarks, but when he said Fez was worth $90... Well I don't know about that, but Zak McKracken was a tricky puzzle game like that, and I bet that was $40-50 brand new. So Fez is worth at least that. It's just we don't pay that kind of money for games like that anymore. I wonder if that's a good thing or a bad thing. $10 is fair for Fez, but I sympathize with Fish when he says it's worth a lot more, because it is.

Nexus: The Jupiter Incident
AFAIC the best PC game ever. Not indie, combined.

Torchlight 2... blows some AAA games' ass.

Minecraft.

Unepic

Antichamber 100%

Dungeons of Dredmor

Hmm depending on what I feel like, Torchlight 2, Bastion and maybe terraria because it's so much damn fun with friends :)

edit: oh forgot to mention rogue legacy, but that game might need something more to do after you've gotten all the upgrades

Super Meat Boy!! :D

Minecraft is da best.

FTL, The Tiny Bang Story, Beep

GTA V

Botanicula & Retro City Rampage :D

Terraria <3

Prison Arthcitect Alpha

Hotline Miami ex aequo The Binding of Isaac

Terraria, Braid and World of Goo.