I might move this over to the main Videogames board, because I've been involved in some travails. Course, I'm not sure how many of you are using 64-bit Linux, so you may not be able to help much.
So far, here's what I've got going:
SDLMAME
Near as I can tell there's really no other version of MAME for Linux worth bothering with; this is the only one still getting development.
Mednafen for NES
I picked this one largely because I had trouble getting the others to work, and because it has Blargg's NTSC video filter. Configuration's a bit of a pain in the ass; there's no GUI and the only way you're going to work out how to set up basic things like mapping buttons is through the README. But I eventually got it working decently. I think. The lag was probably due to the fact that I was doing a huge filecopy in the background.
On the plus side, it's a multi-system emulator, so if I decide I want to play, say, Game Boy or Master System, I won't have to set up a whole new program to do it.
SNES9X-GTK
Way better than the version of SNES9X sitting in the Jaunty repos. (In point of fact, Ubuntu is surprisingly poor when it comes to stocking packages for modern repos. I have compiled more programs from source in the past two months than I have since switching from Gentoo.)
SNES/OpenGL emulators still seem, across the board, to be slightly off on the sound -- it's way better than in the old days, but little things like the fireball sound in Super Mario World get clipped. I hear Blargg's put together a sound filter that will be in the next version; looking forward to that.
Gens-GS
Best Genesis emulator I could find. Decent GUI, good options (including Blargg's NTSC filter). The major bitch about it is that the video filters break when you go to fullscreen. However, it looks like it's got a pretty rapid release cycle, and I'm not the only one who's had this problem, so hopefully this'll be fixed by the next major release.