The 2 emulators I use to run old Megadrive and SNES games on both have Linux ports, but I'm currently using the Windows versions because my winmodem doesn't work under Linux. Sure I could just download them, boot into Linux and compile but there again what would be the point in that? - When I need download any new games I would have to reboot to Windows, why bother? - I can both download them and play them in Windows.
Also as I haven't found any of these emulators in package format so I'd have to fuck around compiling shit, not to mention the Linux nightmare of module dependences.
If your having problems with slow graphics in Linux it's probably because you're using a shitty unaccelerated driver, although most graphics cards will work under Linux you can often have a hard time getting good performance.
Oh and another thing, most good emulators are open-source, the two I use are:
gens - Being part-written in assembly language it's quite possibly fastest Sega Megadrive emulator in the world, it supports 32x and Sega CD games too, unfortunately this is also a major shortcoming as being asm it's 86x only.
ZSNES - a great Super Nintendo emulator, I haven't seen the source but it might also contain some asm code as there is no Mac OS port available.
I conclude that because fastest emulators contain large amounts of assembly code, Mac OS users are penalised far more than Linux users as far a old game emulation is concerned. Also not having fast Linux drivers for some of graphics card is also an issue.