I use HIP
http://byremote.com.au/downloads/default.asp?SCLASS=HIP
to convert play, pause etc Media Center remote buttons to key presses (such as ctrl-alt-p), which VLC can then pick up as hot keys. It takes a bit of configuring and the VLC window needs to be selected, but it does the job.
Write back if you want more info on how I've set mine up.
-Jeepers