@heartbone, I tend to find lot's of uses for transparent windows. When I'm modeling rather than loading the 2d Image into the background, I can keep it right in photoshop and lay down my vertices by making Milkshapes window transparent, or having the image on top and making photoshop transparent.
Sometimes I will be lurking on the forum, but reading other articles or email on the web. I'll set the forum to automatically refresh every minute or so. I'll keep it fain enough to see if someone posts but yet I can read other sites.
I do the same thing if I'm playing online and the game is going slow, like spades for instance. I can be working in full screen on something, but yet can see what everyon is playing.
Some times I'll use it while I'm coding..., if I'm looking at some reference or Pseudo code. I can keep the pseudo code transparent, and work in code surge, both fullscreen at the same time.
That just some examples. Usually ideas come to me on the fly as I am doing something.
Try it out. you'll come up with uses if yout think about it.