I hated that the Earthworm Jim 1 theme was no in the actual soundtrack. The song from the first level is epic and it's not on the soundtrack at all.
I'm pretty sure the music you're talking about is in the soundtrack, I think it's called "Junkit", but I could be wrong.
The Genesis soundtrack will always be my favourite, but I think the PC/CD soundtrack is the definitive version. The PC soundtrack is the "remastered" version of the soundtrack, and is the way the composer (Tommy Tallarico) originally wanted it to sound. I think Mark Miller made the remixes you hear in the SNES version. To me, he Genesis version (also the first version to be released I think) was overall a lot more iconic and had a way better atmosphere than the other versions. The opening of the New Junk City theme here is surprisingly eerie, and the music in Intestinal Distress traumatised me as a kid in a way that the PC version would have completely failed to do.
(PC version: http://www.youtube.com/watch?v=Ww2Lxwhux2o
Genesis version: http://www.youtube.com/watch?v=w12HmyyGg1w
By the way, is that level even in the GOG version? I know its music is not in the soundtrack. :( It wasn't in the SNES version.
The SNES music is okay, I guess. But Gameloft's remixes are pretty atrocious, and none of the new compositions in those games (for the boss fights and stuff) actually fit with the style of the original music at all.