I believe one user on here flushmounted the top of his gamecube to the cabinet so that teh fliptop came out, you replaced teh game, and hit the power switch. Not sure about that one, sorry. I also know Paigeoliver used a CD-rom drive flushmounted in one of his cabs, and it seemed to be rather easy.
An option may be to use HDLoader and save all your games to a hard drive, then just extend the reset switch so you can quickly switch between games.
For controls, both Ultimarc and X-Arcade offer joysticks/buttons-->PS2 adapters, I have no experience with either other than the Ultimarc IPac adn IPAC VE worked great in my cab.
Hopefully there's enough here to get you started. Try searching for dreamcast in cabinet to see what eople have done with consoles. Nanuu has also done a nintendo cab, and if you search in the Project Announcements for Paigeoliver you should find his cab in there.