This is a timesaving one liner if you use Spaces, but I only think it works for Snow Leopard and maybe onwards!
When I start looking for windows in an app, and knows they are in several spaces, then I:
Switch to the space where I want to perform the clean up.
Invoke this script by a shortcut key ^F8 and assigns the app to all spaces.
I switch to the app, and has every window in the current space. It saves some time.
When I am done, I assign the app to a space by invoking the script again.
do shell script "/Applications/Utilities/Spaces.app/Contents/MacOS/Spaces 1"