An app, is an app, is an app. I don't give a flying !@#$ if it's a Qt, Gtk, Python, Perl, Java, Wine, wxWindows, you-name-it app. I don't want every toolkit, library, etc. to invent their own universe with their own little desktop. It would be crazy. You feel the need to group apps to cleanup your workspace: fine, instruct your WM to do it! This does not belong in the toolkit!
Well, you and I seem to have very different opinion on Wine. For you, it's a way to run a particular application. For me, it's like a virtual PC running Windows on my Linux box (ie more like a VMWare or a terminal server / Metaframe approach).
For me, running 'explorer' (or whatever is called the Windows WM) in a desktopped Windows session and actually have the 'Start' button in the lower right corner of the window to start Windows applications would be the way I would prefer running Wine.
Lionel