Here is a handy little script that cleans up WSUS 3 Automatically
[reflection.assembly]::LoadWithPartialName("Microsoft.UpdateServices.Administration") | out-null
$wsus = [Microsoft.UpdateServices.Administration.AdminProxy]::GetUpdateServer();
$cleanupScope = new-object Microsoft.UpdateServices.Administration.CleanupScope;
$cleanupScope.DeclineSupersededUpdates = $true
$cleanupScope.DeclineExpiredUpdates = $true
$cleanupScope.CleanupObsoleteUpdates = $true
$cleanupScope.CompressUpdates = $true
#$cleanupScope.CleanupObsoleteComputers = $true
$cleanupScope.CleanupUnneededContentFiles = $true
$cleanupManager = $wsus.GetCleanupManager();
$cleanupManager.PerformCleanup($cleanupScope);