No idea for mega drive (lol genesis) but for SNES the repo should have the latest version of ZSNES (v1.51? Or is it newer now? Doesn't matter, if it's not the latest, you can grab the source and compile nice and easy). For NES, well, I'm told nestopia is a good option, also FCEUltra.
Additionally, there should be VBA in the repo. VBA is a GameBoy Advance emulator, is SDL based, and should work out of the box. Comes in both command-line flavours and with numerous frontends too.