I posted a script to the forum not too long ago that gets rid of all but the foremost OmniFocus window. Rather than force you to figure out where it is, I'll just include it again here:
I use this whenever I think the windows are starting to pile up.
Code:
tell application "OmniFocus" set mainWindow to front window set frontID to id of mainWindow set background to (every window whose id is not frontID) repeat with thisWindow in background close thisWindow end repeat end tell