CMD-` switches between application windows. That might help a bit, I use it constantly; so constantly in fact, that I remapped buffer switching in emacs to that command.
I'm a hater of the App -> Windows paradigm. I just brought up two finder windows, minimized one, CMD-TAB'd to Chrome, then back to Finder, and finally no amount of CMD-` would make the minimised Finder visible. Plus, just how many mouse actions does it take to tile two windows? Two in Win7, a whole lot more in OSX.
CMD-` doesn't solve the problem, if you are in an application and you want to bring up a window from another application you still have to use CMD-TAB. But this brings up all the windows from the other application.
You're totally right, I just skimmed the comment before I posted, my bad.
Yeah, the best solution here is definitely exposé. Invoke, select just the window you want via arrow keys or beginning to type the window's title, hit return, and only that window comes forward.