As of late, I've come to appreciate the softer low-pass filter of a SBPro card for Doom 1&2. You can listen to some samples recorded by James-F here. Certain SBPro compatible cards have this filter as well, such as the ESS AudioDrive 1868F and OPTi 82C930.

Another thing to check for is proper stereo orientation. Some SBPro compatible cards flip the stereo in Doom, so sounds that are supposed to come from your left speaker end up coming from your right one. Again, James-F did a thorough analysis on this and his results can be found here.

IIRC, Doom's samples are 8-bit 11KHz recordings. They're already quite limited from an audio quality perspective. Low-pass filtering used in some sound cards (per Joseph_Joestar's post) removes high frequencies in the audio source, which can remove some of the noise inherent to low quality samples.

For sound cards, earlier model sound cards tended to have noiser DACs and can be more prone to interference from the computer. Later model AWE32's, AWE64, etc., will sound cleaner in that respect.

I use GUS PnP for sound and SCC-1A (equal to SC-55 Mk. II) for MIDI. GUS PnP has a lot less noise than my SB16 (CT2800).