Try this as a workaround (for Alt only):
System Settings > Keyboard > Shortcuts > Launchers > Key to show the HUD
Click on it and tap just the right Alt key. Now (I find) the HUD only responds 
to the right Alt key and will ignore the left. You can use the left one in your 
VMs.

For Super, you can run CCSM and go:
Desktop > Ubuntu Unity Plugin > Key to show the launcher = (something other 
than Super)

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https://bugs.launchpad.net/bugs/741869

Title:
  Unity/compiz intercepts Super and Alt keypresses from grabbed windows
  like VMs.

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