Aren't there transparent plastic graphics for computer window cases that just stick right on? If so, I couldn't seem to find any, couldn't even figure out the right term for them.
Dude, yeah, those exist. I don't really know their name in English but they're pieces of plastic/paper that can be stuck to any surface (Google says: "Tracing"). You should look for a place that does plotting (graphics, like AutoCAD plotting) and ask them if they can do your design.
I am indeed going to put my logo under my glass desk when I finish designing it (the desk, not the logo, which is already done) and it's going to be a "plastic, rugged sticky paper".