I used to play a lot of flash games of that sort. I'm not completely certain these are all indie games, I apologize if some of them aren't.
The Company of Myself
Shift 1, Shift 2, Shift 3
House of Dead Ninjas (Not a puzzle game at all. It has a sequel, Super House of Dead Ninjas, which is on steam)
Luftrauser (not a puzzle platformer, but whatever - I really like it!)
The original Spelunky (don't think it counts as a puzzle game though?)
Antichamber (a 3D puzzle game)
Hero Core (not a puzzle game either, 2D side scrolling shooter)
gah, I know there were dozens of fun indie platformers I played over time, but I don't have a list of them : ( I found most of them (and these) on the indiegames blog and TIG Source, (and by browsing kongregate). I'll try to remember to look when I get home to get a more complete list.