With the shoes I encountered some issues with the rendering in MH.
The vertices at the inside of the shoes are the cause of these artifacts. Which probably means that MH does double-sided rendering of triangles, or the backface culling does not work properly. Normally these triangles should be removed by the backculling pass because their normals point in the other direction. Their away-facing normal is probably why they are black.
But even if backfaces are not culled, this should not happen, which leads me to think there is something wrong with the triangle sorting or z-buffer. It's very strange.
I also have a theory on why clothes are not rendered properly in MH on the basemesh. A comment by Manuel, "the proxies have no helpers", made me realise this. I suspect that the transparent helpers of the original basemesh are the cause of the clothes not working. (until now I always demoed the clothes on a proxy mesh in MH) The problem could be due to faulty depth sorting of triangles, which is necassary for rendering transparent object, or (more likely) there is no depth-through rendering (do not write on Z buffer) on transparent materials.
Some screens to illustrate this. Note that these are made in in Makehuman, with the basemesh and clothes:
Clothes work on the proxies because they don't have the helpers.
More info about the problem: http://www.opengl.org/wiki/Transparency_Sorting