WinSxS was implemented to eliminate DLLHell.  Applications can use different versions of assemblies without problems.  So over time, this folder will grow, and there's not really much you can do about it, currently.

The net result is applications will be more stable and reliable as more and more applications switch to winsxs. This is a good thing.

• Got a huge bloated WinSxS folder?  Not much you can do about it.
• Can you delete WinSxS?  Nope.  If you do, you'll likely have to format and reinstall all your applications.
• Can you move it to another drive? Not really.  Give your C drive more space instead.

Here's some more information:

http://www.davidlenihan.com/2007/07/winsxs.html