Interesting thread!

Regarding formats supporting vertex colors: I usually use FBX to transfer vertex colors from Blender into ZBrush. Vice versa I export as VRML from ZBrush to have polypaint exported as vertex colors, but there's also a PLY zplugin for ZBrush.

A remark for those of you who are also using Blender and ZBrush: ZBrush uses a different vertex color approach than Blender. In Blender you can fill faces with a sharp border in the vertex colors, in ZBrush there's always a color blend into neighboring polygons when you fill a face.

— Metin