1. FTL: Faster Than Light
It's Star Trek combat THE GAME. Aside from a horrible end boss this game is flawless. I look forward to an eventual mobile port.
It lived up to the hype. What more can be said?
3. Dust: An Elysian Tail
Gorgeous. Just downright gorgeous and it plays really well. It reminds me of 80s disney cartoons that existed long before "furry" was a thing. Plus I'm amazed I LIKE Fidget's character and voice actress. It plays just as well and I need to finish it.
4. Frog Fractions
A hilarious game that is equally charming as it is wonderful to just sit back and listen to. Thanks to Idle Thumbs for introducing me to it and to the Bombcast for furthering it's coverage.
5. Hotline Miami
A filthy game in all the best ways.
6. Mark of the Ninja
The best 2D stealth game.
7. Endless Space
I will begin with my disappointment with it's simplistic starship combat. Aside form that I think all 4X games could benefit from this game's solid UI and willing to edit out superfluous elements that cloud the genre.
8. Torchlight II
I'm not sure if Torchlight counts as indie any more, considering their budget and scope with the sequel but I'll give it credit here because it's wonderful to have a multiplayer alternative to Diablo III.
9. Superbrothers: Sword & Sworcery EP
Gorgeous game that stands alone.