I had this problem too on my EEE 901 laptop with 9.10 Karmic Koala Ubuntu 
Netbook Remix; none of the old solutions I could find seem to work anymore.
However, I found a workaround here: 
http://www.cyberciti.biz/faq/howto-create-keyboard-shortcuts-in-gnome/

Run 'gconf-editor' in a terminal.
Go to apps->metacity->global_keybindings
Find the operation you want and just type "Super_L" (without the quotes) in the 
value field. Log out and log in again.

-- 
No way to bind Super/Windows/Mod4.
https://bugs.launchpad.net/bugs/462737
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