I looked at global hotkeys back in the early 90s for Irix, ultrix and solaris, as it had been easy to do on my Acorn BBC computer. Eventually we decided on solving this in a non-portable way on a level below xlib with some proprietary code.
Since our software installation needed as superuser priviliges anyway, we were able to insert the appropriate software hooks as daemons.
For Linux (nowadays) you should probably look for a software solution by processing the keyboard event on the os level. I would start with having a look here: http://code.google.com/p/logkeys/
A more generic solution would be to have a small PC board with USB in and USB out, which acts to the computer as a mouse and keyboard and translates the keyboard keys as necessary. But this would not be so flexible if you want to change the mapping often.