The "issue" they addressed this time around was the inconsistency of the red, yellow and green buttons that adorn each window in Mac OS X. I certainly hear where they're coming from. For instance, sometimes clicking the red button quits an application (GarageBand and Photo Booth), sometimes it does not (practically everything else). I can tell you that in my day job as a tech support guy, I see countless people who use Windows at home closing application windows with the little red button and assuming they've quit the application (then they can't understand why their computer is so slow, as they've got 11 apps open at one time).
The winning utility by Andy Matuschak and his pal Joe Osborn is called "Stoplight," and it's available here. According to the authors, "Stoplight is a SIMBL plug-in that works via a Preference Pane. It allows you to change the windowing behavior for any and all Cocoa based apps."
Now, before you download, install and experience something very bad, keep in mind: this was written over a single weekend, and should be considered beta (if not alpha) software. None of us at TUAW have tried it. Use a bit of common sense, ok?