This How-To is designed to show you how to most effectively clean your WSUS server of old, depreciated or superseded updates. This how-to assumes that you have already selected the correct update classifications, products, and languages for your environment. If you still need to do that, see this How-To here: http://community.spiceworks.com/how_to/show/2572
Open the Windows Update Services MMC
Select the All Updates View
Set the display to show the Approval status of ‘Any except Declined’ with a Status of ‘Any’. Click Refresh.
Display the Supercedence Column
Right-click the column headers and select Supercedence.
Sort by Supercedence
Left-click on the Supercedece Column.
Select and Decline the Superceded Updates
The updates to be declined have one of two particular flowchart symbols for their updates pictured in the attached image. Select the correct updates and Decline them by either right-clicking the selected updates and clicking decline or by pressing the decline button in the action pane.
Run the Server Cleanup Wizard
Make sure you have all options selected in the wizard and let it run. It will delete the files from the declined updates.
OPTIONAL: Automatic Approval Options
In the automatic approval options, under the advanced tab, there is an option to automatically approve update revisions for previously approved updates and subsequentially decline the now expired updates. I suggest you select them.
At this point, you should have cleaned out a large amount of old, unneeded updates and created plenty of new space.