In the past we used the guide from Kent Agerlund (MVP) for cleaning up the WSUS Database in ConfigMgr, also called the house of cards! This guide is still very popular and of course necessary for having a correct configured WSUS Server. As Kent mentioned, you should do the cleanup task every Monday morning before you start any other work :-)!
But now we got a new option in ConfigMgr 1511 when we setup the Software Update Point. This will allow ConfigMgr to cleanup the WSUS Database and remove any obsolet updates from the WSUS DB.
To enable and run the WSUS cleanup job
In the Configuration Manager console, navigate to Administration > Overview > Site Configuration > Sites.
Click Configure Site Components in the Settings group, and then click Software Update Point to open Software Update Point Component Properties.
Click the Supersedence Rules tab, select Run WSUS cleanup wizard, and then click OK.
Thanks to the MS Product Team to integrate this feature in future ConfigMgr versions!