Originally Posted by
Mr. Smashy
What I would do if I were in your position would be to leave the laptop out of the equation (for now, anyway). I'd also leave the top of the desk open and put the cartridge-based systems (and the Dreamcast) on the top shelves just to facilitate changing carts. Better yet, you could give it a top that's easily removable for when you'd want to place your laptop (or feet, pizza, whatever) on top of it.
The PS2, Xbox, and (I think) Commodore 64 don't need much top clearance beyond their vertical dimensions so it might suit them better to be placed on the bottom. Same goes for the standard NES and just about every other tray-loading CD-based system.