I’m having the same problem as coolbird… However, I already started skinning my character and when through a lot of work while doing it. I know, I regret it now so much!!! I thought that it would be an easier way for unwrapping my textures and keep them organized.
So I have a main torso, a set of legs, a head, and my arms are sepparate (I had both arms as different objects but then I wasn’t able to mirror my vertex weights and envelopes so I merged them into one). I now managed to paint my border vertexes with very similar weights so that there is not much empty space between objects.
Ok, now here is my problem… My plan was to put some cloths on top in order to cover those spaces (and also as part of my character design). So now that I tried to test and similute some clothing, I’m getting some very ugly deformations on those gaps. It’s very bad!!! Do you know of any way that I could fix the problem. Please, I’m very desperate!!! 
I can upload some screen captures if you can’t understand my problem. Thanks!