i was thinking of mounting mine vertically within the shelf i have all of my systems on. The initial concern i had was with the laser and malalignment, but given that the GC is meant to be moved about, i think would be less of an issue. There were no warnings in the GC manual saying that the system must be oriented any particular way either so...
i would suggest some sort of wall mount. The Velcro may hold together, but it may not hold to the wall, especially if it gets hot. i had a dry erase board and corkboard that fell apart due to the heat in my room. You could attach the cube to the mount, or make a sort of cradle to hold it in place, as i'm thinking of doing. This way, it's easy to remove the system if you need (say you want to add a Gameboy Player), and day-to-day tasks like switching games doesn't tax the Velcro's adhesive.
You need to decide how you'll orient it, and how you'll deal with wires. It's a good excuse to get Wavebirds, if you haven't already.