The 3DO version of Doom had the best music (it was in Redbook), but I lost the disc and can't rip it to my PC. I believe the reason the 3DO version had such shitty frame rate was because it was always accessing the CD for the music.
I'd have to say of the pre-Xbox versions I liked the 3DO and Jaguar versions the best, even though they weren't very close to the PC original. The PS1 version's artwork looked different.
One good thing about the Super NES version was map accuracy.
The 32X version had a decent frame rate, but the graphics sucked ass, and it didn't have any more levels than the Jaguar version.
At least the Jaguar version was done by id themselves has good graphics, and the 3DO version has excellent graphics, the marine's head blows up better than the PS1 version and it has a CD-quality soundtrack.