Comment 24 for bug 674138

Another option (that i don't think would be too intrusive) would be to temporarily disable focus-follows-mouse while holding a key (eg. ALT). So if you needed to access a menu for a particular app, you could just hold down ALT while you move you mouse to the menu bar and it would ignore any other window you tracked over. ALT seems like a logical choice since it activates the menus anyway, and I find myself needing to access the menus for non-fullscreen apps rare enough that holding down a key wouldn't seem that much of a pain.