An added note, just because: In Hexagon, there's a sort of... Paint on surface feature. But, it's gimmicky, uses only a sort of "paint from texture map" feature that requires one actually to have loaded up textures at different resolutions if one wishes to actually use a different resolution to paint with and it doesn't play well with most new vid-card drivers... In fact, it's barely worth mentioning because it's so limited and buggy... But, it has the feature, no matter how half-heartedly it attempts to provide it. :)

Blacksmith 3D, sold here, allows one to paint on objects, but I don't think it touches anything close to material shaders and baking those.