Most emulators I've used have worked fine on my "Emulation Station MKII".
Heres a list of what I have working in fullscreen without problems booting from Mahcade.
PCXR (latest 32bit compile).
PCSX2 (works but the openGL plugin is the only problem, not enough people work on it so it's a bit behind DX)
Mupen64plus
Dolphin (latest build), both Wii and Gamecube games work perfectly using their respective settings.
Gens
FCEU (NES)
Mame
Snes9x (works fine for me, prefer GUI to zsnes, zsnes also has 30minute freeze bug.)
So far those are all the emulators I actually want, but I'm sure if I wanted to emulate more consoles I could easily.
There have been many problems settings up a lot of them, but I've worked through them all and fixed them over time. Now they are all stable.
I'm running Lubuntu 14.04 on a Pentium Anniversary with an R7250.