Interesting - I'm actually working on something like this now since my cab is done and I'm nuts.
Originally, I setup my Wii for this purpose (it's modded). The options are basically use the emu's front end itself or use WiiFlow. WiiFlow is good, but the UI leaves something to be desired when you're missing art or have huge numbers of games. Also, PSX and N64 emulation is fairly crappy on the Wii. Anything above those (DC, PS2) isn't going to happen at all. Controller wise, you can readily get an adapter for NES and SNES, maybe N64. There is NOTHING available currently to get Atari/Genesis controllers onto the system, however, that doesn't cost >$50US. (Which is obscene IMHO.). I got this working decently enough that I'm going to get some family members opinions on it when they come over this weekend.
I'm now trying to integrate something similar into my HTPC (a nettop, Foxconn nt330i) using Rom Collection Browser in XBMC. It's working well, is easier to navigate if art is missing, and overall the emu options are better. The 'classics' all work fine (computer power wise) and Project64 seemed to run full speed/fine as well. Adapters are also readily available - I got ones for Genesis, Atari, NES, SNES, PSX for ~$35 shipped. (all seperate, but still...the Atari/Genesis one is for 2 controllers, SNES for 2 controllers, PSX and NES for one controller). I AM however having major skin/XBMC freeze issues due to rom list size so...not sure if that's the PC, my setup, or XBMC.

Note that this PC runs Win7. I've heard that the controller adapters have some issues with *nix based systems, something to keep in mind.