I wanted to have mutiple Gamebases each open a Winamp that is skinned appropriately (NES GB has a NES skin Winamp, Genesis GB has a Genesis skin, ect...)
The answer is to have mutiple installs of Winamp (in each GB "emulators" folder) each with its own skin, (here's the tricky part), with all the skins named the same.
You see winamp keeps track of what skin it is using some where in the registry. So, if you have mutiple installs with skins named differently, every time you open a different install it will look for the previous skin (that isn't there). What I did is to name all the different skins "skin.wsz" and put each one into it's own install dir.
The final result..



I hope this helps someone else.
