For example, when I patched the Rhythmbox, they where specifically hiding the window with their own timing and manually hiding the window. This should have just been done by telling the WM it's being minimized or closed, but instead they created a problem.

Nobody expects the average user to use CCSM for this kind of thing, and I do classify this as a workaround and in some cases a bugaround. I think the shortcoming right now is that WMs are looking at windows without respect to their state. With my Chrome example, I have to make the sacrifice that Chrome won't have any open animations, since it doesn't care about the state of the application.

Thanks for your comment!

Is this not a really big problem? Time and time again I come across programs which don't play nice with Compiz. Sometimes the transparency looks strange because the window doesn't refresh properly. This happens more I think with older software, or commercial applications. I don't think you can expect all users to go into CCSM and add exceptions for all their windows – they'll rather just turn compiz off. Is there an elegant solution to this problem?

Another issue is with programs which minimise to the system tray when they are closed (Amarok does this, Rhythmbox probably does it too). The zooming effects to zoom-to-taskbar for minimising are very good, since they show the user where the window has gone. But it doesn't work with the system tray – compiz assumes the window has been closed and applies the corresponding effect.