My mail server has thousands of shared IMAP folders, and Mail.app has no notion of "subscribe/unsubscribe" folders -- it simply presents you with all folders visible from your namespace. If you click on a folder, Mail.app will attempt to synchronize and cache that folder's messages forever. There is no way to unsubscribe or selectively stop caching, but...
If you remove the folder(s) that you want to stop caching from ~/Library -> Mail -> IMAP -> your_user@your_domain.com, then Mail.app will stop caching that folder ... that is, at least until you click on it again (so don't do that!).
This was very helpful to me, as my Mail.app was attempting to synchronize folders containing a total of over 3,000,000 messages.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050616115554851