Hmmm.... OnTopReplica does exactly what you want, just seemingly limited to a single clone. The major (read: MAJOR) issue is that it only supports Win Vista/7... No XP support, which won't be much of an issue in a few more years (hopefully), but it will be for many people at the moment (my rig is xp based for example)...
However! I will be tearing the code apart in an attempt to figure out how he captures image of a minimized application. Hopefully that part doesn't require DWM (Aero -- I turn it off on my win7 boxes to increase performance)...
GRRR! You have just caused me hours and hours of reading/research/experimentation... *shakes fist in mock anger*
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