While I would still like to see this fixed, I have found a workaround
(that at least works in 12.10):

- In compizconfig-settings, enable the 'Extra WM Actions' plugin

- in the options for this plugin, enable a bindkey for the 'Toggle
always on top' option (I chose ctrl-F9)


Now you can open the application and its fullscreen window. With the fullscreen 
window focussed, press the chosen bindkey. Now you can focus another window or 
app on the other monitor, and the fullscreen window will stay on top on its 
monitor.

I've tested this for both libreoffice-impress presentation fullscreen
window, and totem in fullscreen mode.

Note that other windows showing on the same monitor as the fullscreen
window will NOT now show, even if you focus them (e.g. using an Alt-Tab
sequence). This is to be expected, as the fullscreen window is now
marked as always on top. However if you arrange for the other window to
also have the always-on-top attribute, then you can then use Alt-Tab to
flip between them.

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https://bugs.launchpad.net/bugs/748539

Title:
  Multi-monitor - Panel and launcher visible on top of multimonitor non-
  focused fullscreen apps

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