I did something similar putting a PC10 and a VS super mario in a cabinet..
I used relays, and a flip flop to drive them, so its just a toggle button, no powering down or whatnot..
Wiring all the joys and buttons together is no big deal, these are active low, in other words, you're just grounding them out, not switching voltages.. All the multi-jammas out there just tie all the controls together.
Video and audio are another problem though, well, video was for me.. The video signals tied together came out all washed out and blurry.. I used two CD4066 chips to switch them (Quad bilateral switch).. Basically, these are just digital switches, I tied all the activation lines together, powered each with 12v and ground, and by sending 12v to one or the other, I allow signal through that chip..
Diodes did not work to isolate the video signals, as I read in a Bob Roberts article. The 0.7v or so voltage drop made it look awful, it was better without them. Nintendo boards are negative video, maybe a positive video would work better with diodes, but the 4066 chips have an "on" resistance of a mere 100 ohms, which is negligable, and both games look crisp and great when running.
In my case audio wasn't amplified, and tying the two audio lines together wasnt a big deal, although the VS is noticably louder. A solid state relay, or another cheap realay would be a good choice for switching audio, and from what I can see that's what the commercial solutions do. I wouldnt recommend splicing amplified audio like this, since that may do some damage. In this case, I'm probably going to add a couple of 10k pots to attenuate the volumes to match, but most boards out there have volume onboard.
Although it works great, my home-wired on perfboard solution is a friggin mess of wires, I will say that much. Maybe you're neater than I am, but four boards would be a nightmare to do the way I did, but still doable. Mounting the boards and wiring the harnesses was the real killer, the electronics involved aren't complex at all.
Relays (or mechanical switches) for power (12v and 5v, -5V if needed), CD4066's to switch video (or more relays), relays or switches for audio.
Of course, none of this is any good if your monitor wont sync all the games, so make sure you try 'em one by one by themselves and make sure you dont have to adjust it for each game...
I plan on making more multi-cabs, and am looking into having some boards fabbed by expresspcb.com or a service like that. I did start noodling around some layouts, and I'm thinking a 4-board pcb would be a good goal, as I could keep the size down, and I dont see how I'd manage to mount 8 boards in any of the cabs I own. I like the stuff I do to look "pro", or like it was designed that way.
I have all the cabs I'm ever going to fit into this house, yet want more games, so it's the way to go for me.. (Neo Geo + Neo Geo 64 + Atomiswave, CPS2 + CPS1, etc etc etc) I want to make it optional whether boards are all powered, or power is switched (for tight spots where multiple psu's aren't feasible, or other reasons) - I can think of cases where either scheme is better.
It's late, I'm rambling and not thinking too clear, but I'll post some schematics and more info on what I did later, and keep you folk up to date on the progress of my proposed DIY-boards, I figure if there's enough interest, a small run of 20 or so would make an attractive alternative to big-$ solutions..
In the meantime, I need to get a CPS2 and an F3 system ready for xmas (XMen vs SF for the boy, Puzzle Bobble 3 for the girl), so my short term goals involve painting and finding artwork and t-molding and new buttons and patching the F3 to play in US and all that good kindsa stuff.. I'll be on this, though, because I definately want to get my Neo/Hyper Neo machine in effect, and do a proper double or triple donkey kong (no cheesy chipstacking hacks where the sounds aren't right)... I want to add a mario bros (original) and popeye to the nintendo cab I built, etc.
If any of that jabbering made sense, woohoo.. If not, I'll be back later.