I had the problem of disappearing preference panes (in my case: Classic and Accounts). I think it happend after installing a Preference Pane item.
Solution: Close System Preferences. Go to home -> Library -> Caches and remove the file com.apple.preferencepanes.cache. Start up System Preferences again, and the missing panes should be back.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040215101202922