As much as we'd like our front end programs and key mappings to cover everything, sooner or later you're going to have to deal with Windows, or a menu, or something (the menu's in Burnout Paradise are worst I've seen so far. game is great, menu's are horrible).
On the driving cabinet, I don't really have room for it. I'm using a wired mini-keyboard and trackball that I put in my lap when I have to deal with it, then set them on top of the computer case while I'm driving.
Most of the newer PC games require keyboard / mouse interaction at some point. (username / password, clicking some stupid button that doesn't have a gamepad input option, etc).
How do you guys deal with this? On my upright MAME cabinet, I've got a keyboard / mouse drawer that rolls out, very easy, almost invisible.