The Windows key is still useful under Linux. My window manager, and I imagine most others, can use it as another modifier key. I think it maps to Hyper in mine. I have it set to do all sorts of things when combined with different letters: open an xterm, toggle window maximization, display the WM's window menu, etc. It's a nice place for shortcuts because it doesn't get in the way of regular application shortcuts like Ctrl or Alt would.
On the other hand, I have not used a program in the last 10 years that used F12 for anything. That key got my vote.