How can I make Super+M and Super+S work for compiz effects and not for indicator applet & indicator applet session in Lucid?
If you are brave and know what you are doing, you could use one of the patches listed in bug report #558581.
You could also use
indicator-applet-complete which only uses the Super+S shortcut. See this answer for more details.
You can change the key combination of each Compiz effect inside CompizConfig Settings Manager.