When in Preferences (in WGM), you can manage each preference by user according to never, once or always. (this is done by going to the Overview tab when configuring a users Preferences in WGM). This displays a GUI for managing the Apple-related preference.
Tiger introduces preference manifests, which allow you to specify managed preferences for both Apple and non-Apple applications, displays a more advanced and detailed option in a generic list view. (You go this in the Details tab when configuring Preferences in WGM)
When Preference Manifests (from the Details tab), add an application, then click Edit…. This will open the Preferences Editors (the info is displayed in a generic window and is grabbed from the Applications plist). Unlike above, the options here are: once, often, and always.
When a particular preference is set to once, the first time the user logs in this preference will be set this way and the user can make a change that will stay.
When a particular preference is set to often, the preference will revert to the managed setting each time the user logs in, but will allow the user to change the preference setting while logged in for that session. When logging in again, the preference will revert to the managed setting.
When a preference is set to always, the user will probably not be able to change the preference setting at all (it will always be managed by the preference manifest rules), even while logged, but some Applications do not honor this will in fact allow the user to change the settings.