Honestly, I find the PC soundtrack to be much nicer. Tangerine (one of my favorite video game themes) has never sounded better. I was amazed to hear actual electric guitar in the song. I grew up playing these games on Genesis. For me, this soundtrack is a huge step up.

One thing I did just notice is that during the "follow the sequence" section of the blind salamander level, the music doesn't change like it did in the Genesis version. It just continues playing Moonlight Sonata. That disappointed me.

Alright, it's just your nostalgia. SNES port wasn't very good. It had some nice graphics, but yeah. the rest of it wasn't really a dream come true (the second game is much better in that regard). The soundtrack of SNES version was... pretty much horrible. It sounded really, really damn off. The music in PC version was taken from Sega CD (EWJ) and PSX/Saturn (EWJ2) versions respectively and was composed by the original composer, Tommy Tallarico. If you compare Genesis version (which is the original version of the game, SNES is a port) of the soundtrack to PC, you'll see, that they are actually very similar.

Little comparison?

New Junk City
Megadrive / Genesis
http://www.youtube.com/watch?v=BtkMPseIwa4

SNES
http://www.youtube.com/watch?v=fLKY1DtBd-Y

Mega-CD / Sega-CD
http://www.youtube.com/watch?v=VCbEBGcPagA

And Vagabond, i want to slap you for saying SNES soundchip was bad :)

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.

Intestinal Distress was sadly a level that was exclusive to the Genesis. I believe the level was also released in the special edition (which is where the remastered version of the music came from). Still, I could be wrong. I haven't played far enough to see if it's in this GOG version. The music is definitely not in the soundtrack.