I've gotten Star Control 3 working with solid sound for speech, although the cinematics still have stuttering sound. I have VDMSound set to the Soundblaster 16 setting, but in the Star Control 3 SETSOUND setup program, I have digital audio set to simply "Soundblaster compatible" (it's the most "basic" soundblaster setting). Make sure you're running the setup with VDMSound as well. Using these options, I get solid non-stuttering sound for any speech outside of the cinematics.
Also, it doesn't hurt to run the game from a virtual drive, as this game does an awful lot of in-game loading from the CD.