Just look at the photo. My first reaction is - "Man, I hate when I get a brand new computer and it comes preloaded with all this random bloatware". Then you realize it actually is part of Vista and a little bit of your geek soul dies.
Even apps that share the same look are different, Mail and Calendar - Search box is in a different place. Media Player and DVD maker, both are black one has a much fatter bar for some reason. Even the back and foward arros are different on these apps!!
Vista - Clear Confident & Connected. Apparently not the development teams working on it. Maybe if they only had it prior? Chicken or the Egg? :)
All kidding aside - the best thing to do here is really start over. Do not try to fix a trainwreck - you will spend more time on it than you think and your result wont be as nice. I do not know how MS develops, I would hope the UI is very disconnected from the actual logic, say in an MVC style. But, since this site is sort of asking my opinion this is what I would do:
Design two looks, that work well with eachother, I have found that application's that are "editors" (DVD maker, Wordpad, etc) need different UI than those that are "browsers" (Web, Explorer, etc). Borrow from Office 07 for the editors, and the tabbed look for the browsers, but really - PICK something. Sometimes apps will need both, say Mail, one to browse the messages, another to create a new one. But the point is there are only two designs, which means less to learn, and 2 is better than 10 to make work for continuity sake.
Secondly, Blue to me does not mean Communication, Black to me does not mean media, just as Blue Grean does not mean files. All together it looks a mess. I want to control these colors by the theme. Applications contents (not to mention window title) are usually more than enough to help me at a glance find a window (think Excel vs Word).
Let me pick a colors (like the fade in the explorer windows) for the toolbars OS wide (if this stays, and I think it should in some fashion). As an added bonus - you can make the active window have a much richer color, and the inactive window have a more faded version as there is another complaint about figuring out which window is active.
Also, another nice feature of that other OS is color coding of folders, at least the names. I think it looks terrible (some background highlight on the name) but I think it would be a good use of color to change the color of the actual folder icon, sort of like color coding in outlook - and that overrides the default gradient in the toolbar for quick visual reference when open!!
Apple in the past has been accused of terrible consistancy but they have almost killed the brushed metal and the rest of the OS is really starting to follow one or two concepts, and all the third party devs are jumping in line behind them - this can happen, needs to happen on windows!!!