Many people bring up Cave Story as the example of the ultimate indie game...
It was made by one person, etc... And man, it SHOWS. Sand Zone is a friken TERRIBLE level, and getting all of those dogs is not fun in the slightest. The level design gets grating on multiple playthroughs, really hampering its enjoyment factor over time.
Plus the arcane and obscure requirements to "save Curly" is not exactly an example of good branch-making... if that's the right term. So... the professor lives if I -don't- talk to him? How does that make sense? Nothing in the game alludes to the fact that you shouldn't talk to him- you have to be an asshole and just leave him to get the "good" ending. Or not leaving Curly to rest. Um, what? The book in the house says "let her rest" but she dies if you do. Nice job Pixel-san!
I don't hate Cave Story, but people often forget the glaring flaws in the game (that will never be changed because of its status as the indie darling, ha ha).
Braid is just boring as all hell, and its touted "story" is completely rubbish. Mr. Blow-hard is much more accurate. :p
Iconoclasts is great, though. Hopefully one day it'll be finished.
If you want some good indie/doujin game lovin', check out Crimzon Clover. Man that game is awesome.
There's a free version (first three levels), but it's made by one guy and damn is it a fun game.
Same thing with Kamui. Another great doujin shootemup.
And it's free, if I recall correctly. Get it, and you won't regret it.
I like an indie game that actually tries to challenge me. Or is just plain fun.