Basically, there are pro's and con's to each option -
One cab and swappable panels - Pro's: Nice clean layout, optimized for each game. Only one cab to deal with, so less space and expense. Con's: Panels/Modules need to be stored somewhere. Sometimes is a pain to swap around if you play a lot of different games, e.g. "I got my Pac-Man fix for the day, I feel like playing Centipede, but not sure I want to dig out the trackball module and plug it in, or just fire up a quick game of Time Pilot instead.
One cab with FrankenPanel - Pro's: Less space and expense required, avoids the hassle of swapping controls around. Con's: Generally doesn't look as "clean". Tough to get a layout that works for "all" games and even if you do, it will probably be sup-optimal for "some" games.
Multiple cabs - Pro's: Allows you to have multiple control layouts and swap by moving to the appropriate cabinet. Control layouts are more optimized. Multiple games can be played at once. More similar to having a real home arcade. Con's: more expensive, more space required, harder to justify to non-arcade game nuts in your family.
Hope this helps!!! If I could do it, I think I would lean toward the multiple machine option.