It's almost unfair to include Minecraft, kind of cheating since it's so much more than just a game.
So asides from that, my top indie game from the original humble indy bundle would be Aquaria. Just an awesome game all around, and anyone who enjoys the Metroidvania type of gameplay owes it to themselves to play it. Runner up after that would be Recettear. Mount and Blade would likely be up there as well I just haven't gotten around to gettin it yet.
And speaking of indy games, I'm always on the lookout for good rpg's, like Recettear or Eschalon Book 1 & 2. Last weeks extra credits about game awards showed at around the 3:15 mark showed quick screencap of what looked to be one, with the implication that it was worthy of some kind of reward. I asked in the thread and after sent a direct message to them, but no one responded to me on it. Anyone know what game that is?