I guess I'll be another person apologizing for posting in such an old thread, but it is on topic.
I managed to acquire the actual discs for several of the different hardware versions (though the conversion files still came in handy when the ATI version wouldn't recognize the hardware and I had to install the Pentium version and install it) and installed a couple of different versions, some on the same machine. I found that it's actually possible to copy the mw2.prj file from different versions and get them to work. This is interesting since the ATI and Matrox versions have significantly different textures compared to the 3dfx and S3 versions (at least in the Mesa Desert). So, here are the results of what I was able to test:
Using the 3dfx version on a Canopus Voodoo1 and dgVoodoo on a Voodoo5 (I'd expect dgVoodoo to be the same on any D3D card, and the dgVoodoo results were exactly the same as the real Voodoo1)
MW2.prj file tested:
PowerVR: fatal exception
ATI CIF: works, but sprites (explosions, etc.) are slightly discolored
Matrox: works, but sprites (explosions, etc.) are slightly discolored
S3: works
Using the ATI Rage CIF version on a Rage Pro Turbo PCI with other MW2.prj files:
PowerVR: fatal exception
S3: works, but sprites are discolored
3dfx: works, but sprites are discolored
Matrox: works, but textures are striped
Using the PowerVR version on a Matrox M3d:
All: fatal exception
The 3dfx version is the most accessible, since using dgVoodoo or another Glide wrapper allows it to run on just about any video card that will run on a compatible OS, so it's nice that it appears to be the most compatible. It also allows for 800x600 resolution, so the 3dfx version with the ATI mw2.prj file looks significantly better than the ATI version running on native ATI hardware (discolored sprites aside) and has a much better frame rate.
It's also interesting that the ATI and Matrox versions are very closely related and the 3dfx and S3 versions are very closely related. They have similar textures and compatibility.
The disappointment is that the PowerVR version (arguably the best looking version overall) mw2.prj did not work when used with the 3dfx or ATI software.
I also have the Matrox Mystique conversion files if anyone would like me to upload them to this thread. I do not have a Mystique card to test them with, but they're the same 4 files used to convert to the other versions. I also have the Pentium Edition files in case anyone only has a hardware version and wants to run the game rendered in software.