What is annoying about this is that you have to be in video mode in order to make the player on top. You can't do this while playing audio. I actually downloaded a free WMV file off the Internet just so I could play the file and then mark it as "always on top." Then I switched to audio.I wish that the VLC team would fix this so that those of us who mainly use VLC for music could mark the player as "always on top" without this workaround.
you could start the player with --video-on-top switch (did not actually test this).