For me it's a tie between Braid and FTL Braid reminds me a lot of Super Mario Bros. and I believe it's meant to. Some of the art and level design is obviously a parallel to Mario. The twist is that you can manipulate time. It creates some of the more difficult puzzles I've ever played in a game (the hardest was Space Chem). To keep it interesting, the way you manipulate time changes between each world. Some were easy, but some were incredibly challenging. And to finish it all off, the end of the game was incredible. That's really all I can say about it without giving anything away. FTL is a rouge-like game where you captain a spaceship. What drew me in was how I hoped I could command all the aspects of my ship in battle like Admiral Adama from Battlestar Galactica and I wasn't far off. What kept me playing was how addicting the game became. There were so many small stories to find through it and so many things to discover that I regularly go back to play it. I have to warn you though, it usually takes a long time for your first win. It's difficult and sometimes unfair, but it is extremely rewarding when you finally win.
Braid's puzzles were really, really good. What I loved more than the puzzles was the way Braid taught you how to play. The game basically teaches you each level's mechanic in each world's version of The Pit, then gradually teaches you more. It's never explicit, they let you figure out the way things work through puzzles, through trial and error, until finally, the last few puzzles of the world put it all together to test what you've learned.