Mostly, we see success in the indie 2D world:
Don't starve - http://www.youtube.com/watch?v=MsWm_gWyk4s
Binding of Isaac - http://www.youtube.com/watch?v=c5PLC6nmOO4
Terraria - http://www.youtube.com/watch?v=GHPX0kR9h7I
And just released Starbound - http://www.youtube.com/watch?v=ZvrmB4tw33Q
Certainly 3D games are quite exciting in this space, too, but the 2D games seem to have a lot more traction with the big exception of minecraft.
I suspect it's simply easier to make an engaging sandbox when you don't have to worry about complexities in art assets that a 3D game requires.