Better Solution
Sorry to resurrect this old thread, but I had this problem recently and the solution offered did not help. Actually, my controller was not too far off-screen, it was just gone. I went through all the above motions in the menu bar, and tried the screen re-sizing trick to no avail.
This solution worked, and will reportedly work with any problem of a controller in any app that has disappeared or moved off-screen:
Turn off your DVD player. Go to the Users folder --> Library --> Preferences folder and find the file named "com.apple.DVDPlayer.plist" and trash it. Re-start your DVD player and the controller should re-appear.
I am posting this because I found three other forum threads on this topic on the web and none of them had the solution. This was found by looking for a solution to any controller no longer showing on the Mac.