What's this thing near the sunroof motor?
 

That long metal rod doohicky looking thing. :P

What's its purpose? I had to keep moving it out of the way to remove the trunk liner to get to the antenna. I don't like moving it too much, it feels kind of loose, but it's still tight fitting to whatever its secured to.

I believe that's the sheath for the sunroof cable/link. It supports the cable/link so the motor can either push or pull on the sunroof.

Could it be the crank for manual operation...
 

when the motor fails? I defer to Pete....

That tube (as stated 2 posts ago) is the sheath for the cable for the sunroof.

Its basically like a window regulator sheath (manual windows) so that it protects the cable and makes it enter at the correct angle.
Don't bend it too much or it will either break off or bend. :)