Since the talk has come up, I should make it known that MainMemory from Sonic Retro put the original music back in the PC version
, and beyond that, it's very easy to dress up the MIDIs with soundfonts now that it's not the year 2000 anymore. That link also has another link to the HQ hack that allows for custom soundtracks, so it could go even further. The PC version would actually be a viable option and could be an incentive for soundtrack donations since we can customize it completely with the HQ hack. $20 for replacing Carnival Night with Numa Numa or something, perhaps? $20 for Hard Times Ice Cap?
The only thing I'm aware of that doesn't work on PC or Saturn is the horizontal wrap in Marble Garden 2, as the PC and Saturn ports of the game have a different behavior for going over the ceiling that doesn't allow the zip. It actually opens up a nifty trick in Launch Base 2, though, although I believe there's already a horizontal wrap there that negates this advantage.
I do agree with not using Gens, though, especially after our long discussions about emulator accuracy. The PC version would be an official port, but if we're emulating, Regen and Fusion would be the emulators of choice for accuracy and even have better default screen filtering than Gens. They also don't enable the "better" (read: worse) PSG interpretation by default, although I'd think anybody here would be smart enough to disable that.