For Oneiric we went the easy route of adding a way to run external applications for the stuff we wanted in the control center. But this looks quite bad (some panels are embedded, others run a separate application), so for P I'd like us to do a cleanup and avoid as much as possible having external windows.
So, here's a list of what we have:
the tricky one is Ubuntu One, so I guess we'd have to leave it as it is, or write a panel that just embeds the u1-panel window?