He built a custom box out of plexiglass, added some mounting brackets in it to hold the systems, and then cut holes in the sides where it was needed (tray's, controller ports, power buttons, etc)
To get something like what you're talking about to work in a standard tower case, you'd need to first take the whole system apart, and possibly replace the DVD drive's with standard ones for a PC (which would also mean the systems would need to have a modchip).
I've seen one where someone stuffed an Xbox and PS2 into the same case, and they were working on a version with a GameCube but at the time no modchips were available for GameCube's so he was having to import the Panasonic Q (Japanese GameCube+DVD Player system), and try to implement that drive. It was pretty slick, he had the controller ports stacked on top of each other in 2 of the 5.25" bays, and DVD drives in the other 2 5.25" bays. The motherboards were mounted to each side of the case, and their respective switches/power buttons were mounted in front and the power supplies mounted in back, as well as all the audio/video hookups mounted in back.
... and it appears to have vanished from the net, as I can't seem to find a link to it anywhere. Closest I've gotten is just an Xbox put into a PC case
. But you can see how the same/similar methods can be used to mount a PS2 to the opposite side. And this one uses the Xbox DVD drive, so it can
be done without a modchip ... but why would you want to?