While the Preferences utility is missing, this may be a simple oversight on Apple's part.
Most preferences in OS X are stored directly in the user's Preferences folder; however, within this folder is a directory called ByHost that contains other commonly used preferences.
In OS X Lion Apple has added a new option for customizing the system preferences, allowing you to conveniently show or hide individual preference panes.
When application settings do not stick in OS X, it's easy to just remove the preferences file; however, sometimes it's useful to investigate the problem a little before doing this.
Apple's Magic Mouse has special system settings for managing its multitouch input surface; however, sometimes these system settings don't load properly.
Several users have experienced an issue where System Preferences will not open properly or freeze when opening in Snow Leopard.
Government policies that express preferences for open source can help fuel adoption, but government mandates arguably achieve the opposite.
Applications in OS X save preferences to property list (.plist) files in various preferences folders; however, sometimes multiple copies of a specific plist file may accumulate in the same folder.
System Preferences Access
One relatively rare problem in Snow Leopard a few people have experienced is a corruption in the Displays system preferences that results in a "do not localize" message listed in the resolution list.