I suggest using one at least of these two characters from "Little Fighter 2", as a playable character for this game, but that's up to you.
Julian (Little Fighter 2)
A well balanced character with a limited, but powerful moveset.
Davis (Little Fighter 2)
A well balanced character with a moveset focused on dealing combos.
The trouble with the LF2 characters is that they're very generic, and seem designed more to fill certain niches (sword guy, ninja guy, fire guy, archer guy) than to be unique, iconic and memorable characters in their own right. That said, LF2 is a pretty well-known game, and as a beat-em-up, it has many similarities with Indie Brawl.
I think it's at least worthy of a support character. Davis, who apparently has his own action figure, is probably the most iconic character from the series, but Julian would be my second choice.
Runman's high speed could make him an interesting character, and there's probably just enough material out there to make a movelist out of. I still think he's best as a support character, but I could see him working as a main character, too.
Machinarium is great, and I do think we need to include something from it. A stage would make the most sense, but that is a bit redundant with Samorost Island. The trouble with Josef as a character is that he is nonviolent and has no moves that resemble attacks. I could see him as a support character, but I don't know what he would do.
Commander Video (Bit trip series)http://www.bittripgame.com/
I haven't played these games, but Commander Video doesn't seem to have too many moves. You could probably make a move list for him, but he seems more suited to be a support character.
Outside of standard running and jumping, his only ability is altering the flow of time, which is absurdly broken for a main character. He'd make a great support character, though, which is why he's on the list.
It's a line that can flap and spin. I don't even know what it could do as a support character.
He's pretty generic, especially in terms of attacks. Minecraft is much better suited to be a stage.
Never played it, but it doesn't seem like Dim can do much more than run, jump, and change dimensions (which is inapplicable to Indie Brawl). As far as Matt Thorson's games go, Runman, the bird from An Untitled Story and Ogmo are the most iconic characters.
Again, the issue is that Toribash fighters are designed to be as generic as possible, with few distinguishing features.
He can't do anything but run and jump, so he can't be a main character. He is planned as a support character, though what he actually does has yet to be determined.
What I said about Dim basically applies here as well.