Thanks for the ideas! I do think I'll make some sort of place for the remotes to go. They're pretty valuable (50$ a set!) and they are already getting put wherever people drop them. I'm learning to sew so this seems perfect for a project.
The shapes of the controllers are a little weird, especially the nunchuck. I really don't know how to describe its dimensions.
The other idea I had was from Craft: http://www.craftzine.com/blog/archive/2006/11/diy_laptop_decals.html
these decals seem perfect for the side of the Wii. I don't know what I'd put on them though.
New ideas still appriciated!