I got The Swapper over the weekend, keen to try it out.
The Binding of Isaac still tops my list
*cough cough* shameless self promotion *cough cough*
Blazin' Aces:
http://www.reddotlab.com/blazinaces/
EDIT: I'm in the process of HD-a-fying it, sneak peek:
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oh yeah, and my latest favourite indie games, Strike Suit Zero/Infinity
Maia looks really interesting
http://www.maiagame.com/media.php
Yeah indie is about the developer, not the publisher. For example I don't think anyone would argue that Bastion is not an indie game, and yet it was published by Warner Brothers.