I have some skirts and tops that don't clip in Bodyshop or Milkshape, but are clipping in game.

Is clipping in game due to bone assignments or the meshes being too close to each other? If I shrink/widen the meshes any further then they're going to look weird.

Does anyone have some tips on getting rid of in game clipping?

Would you mind sharing screencaps of them? In my experience it depends on the model.

You can reduce a lot of clipping with careful bone assignments. I do mine in Blender since you can 'paint' them manually and copy/project them between meshes. It also helps to 'stress test' your work by going into animation mode and trying different poses.

Some clipping is impossible to avoid when you have overlapping mesh bits, though. See the base game hula skirts. If the body geo isn't gonna be visible, I just delete it.