So I was running Enhanced Edition with the WeedsGM3 soundfont, and when it got to the guitar part it sounded incredibly weird, like there was way too much overdrive in the guitar instrument and it sounded horrendous. I went back to my old DosBox version I had set up and when I used the same soundfont, the guitar sounded much softer. I even opened up the SS midi files on the GOG page and they sounded exactly the same as the DOS version when played with Windows Media Player + WeedsGM3 emulated with BASSMIDI. Any reason why this might be?

OK then. If there is a problem it should me made specific. Who feels like using MidiOx (http://www.midiox.com/) to record the exact midi data stream of both SS1 editions, and then to compare them?

Classic is configured by default to play music through a virtual Sound Blaster 16. I have gathered from other threads that it is not even playing the same files when it is configured for General Midi, and I presume that EE is playing the General Midi tracks too.

I'm on level 9 now and during my playthrough I have tried various soundfonts but haven't really found one that sounds good throughout. Of those that didn't immediately sound awful the songs played fine for the most part but every now and then there is a bit that doesn't quite sound right. Theres also a few places in the game where ominous ambient starts playing along with the music, and this hasn't sounded very good with any soundfont.

I have started to wonder if the music was really made for the OPL2/3 synth and later quickly adapted for general midi as an afterthought that didn't receive enough attention.

This is correct, and I don't really understand why they bothered with GM support. I can't imagine playing System Shock with no sound card and just MIDI, and didn't pretty much every DOS compatible sound card either have native OPL2, or in the GUS's case, emulation?

I ended up using the arachno-soundfont and the music sounds pretty good.

Its a bit of a pain because the overdrive makes the midi sound a lot more unpleasant compared to the other GM version I had set up. If I was able to play the DOS Enhanced Edition with 1920x1080 then it'd be fine, since 1920x1080 looks great and the GM too.