I've also found this problem, and looking at the code it seems that most of the linux external player handling has yet to be written - including the forceontop option.
However, there is a workaround to get mplayer on top (this is using the current svn):
- firstly, you must be using kde (I've done this is kde 3.5, no idea if it works in kde4)
- secondly the external player options in advancedsettings.xml have moved to .xbmc/userdata/playercorefactory.xml in the very latest versions - see
http://wiki.xbmc.org/?title=HOW-TO_use_a...a_playback
- then, start xbmc in a window, and right click on the title bar and select Advanced->Fullscreen
- xbmc should now appear fullscreen but mplayer will still appear in front