A long time ago, I had written up a little script that uninstalled VS - this is pre-pre-pre-release Whidbey, and setup at the time had a few problems with things it left lying around. One of the things it did was clean up some of the entries in the WinSxS folder that had been left around.
Yesterday I was needing to do a clean VS install and took the same route, except now I'm running Vista and Whidbey has shipped so there's likely no actual need to clean up WinSxS myself. While I won't go through the process, you can't just delete the files, there's a few steps involved first (so you don't have to worry about just accidentally deleting contents from there).
Long story short, it royally busted up my Vista install and lots of apps on top of it (like, well, Office). Since the affected files were part of the 2.0 framework's support files, I tried to go the route of using dotnetfx.exe to do a repair, but that didn't work with an error that it's part of the operating system (which is true). You can't turn 2.0 off and back on and reinstall that component, either.
The good news is doing an upgrade (yes, from Vista RTM to Vista RTM) fixed everything and the machine is happy again.
But the key summary is - don't mess around with WinSxS - later in the day I got some nice explanation emails about how WinSxS is maintained automatically, so leave it alone, kids :)