I'm currently developing with a company-bought Ubuntu laptop after having used OS X for the last three years almost exclusively. Like Windows and OS X, it pretty much demands the use of a Super key for accessing OS functionality and popping up utilities and applications.
I used two tools to do the remapping, xev and xmodmap. The lower-left control key is key code 0x25 (37). Ultimately it ended up being simple, and my .Xmodmap looks like this:
keycode 37 = Super_L
add Control = Control_L Control_R
I also added the following to my .xinitrc, but it may be redundant:
It's more awkward than a proper Super key, but it's workable, and I'm typing happier.