With ControllerMate installed, you can access any of the Remote/IR Port's button presses. However, the problem is that the commands are still being sent to Front Row: even with the perfect VLC setup, hitting Play would both stop VLC and start iTunes -- not a solution.
Finally, I realized that ControllerMate shows "different" button commands for Fast Foward and Rewind (holding the left and right buttons, as opposed to just pressing them.) With this in mind, I found out that pressing and holding the menu button also counts as its own button -- a button not used by Front Row!
In ControllerMate, drag in the Apple IR 'Menu' item and link it to the following AppleScript:
tell application "System Events"
set myApp to name of first application process where frontmost is true
if myApp is "VLC" then
tell application "VLC" to play
else
tell application "VLC" to activate
end if
end tell
This turns holding the menu button into a VLC controller, opening VLC if it's closed, and play-pausing it if it's open. Until there's a way to use all the Remote's buttons, this seems to work for me ... and of course, you can have that one key do other things, too.

