My memory may be faulty, but I did try to get D2 3dfx and the D1 3dfx Beta (available here) to work with a Voodoo5 5500 under Win98SE about four years ago.  As I recall, both patches worked.  The only problem I recall was the fact that the PIII 933 MHz system I was using was too fast for the game (at least for D1, I can't remember if D2 had the same problem or not).

I do remember that both games looked absolutely beautiful and modern compared to the software rendered versions.

Edit:  I just loaded D1 and D2, patched both games to the latest versions, and applied both 3dfx patches, and they seem to work just fine.  By cranking up the anti-aliasing to 4X at 640x480, the speed seems quite good.  Without the anti-aliasing, D1 has the ship bobbing up and down at an insane rate.  I can't seem to take screenshots using the Print Screen key within the program unfortunately.  Obviously, I haven't spent too much time testing it, but I haven't seen any issues with the 3dfx patch.

I did have to drop the screen resolution to 640x480 and 8-bit color in order to apply the D1 3dfx Beta patch.  At 1024x768 and 16-bit color it would die without performing any updates for some reason.

This machine has a Soyo SY-7VCAE motherboard and a Pentium III 933 MHz processor.  OS is Win98SE and DirectX Version 7.  Sound card is a Creative Labs Sound Blaster Live! CT4760.  Video is Voodoo5 5500 AGP.