Comment 1 for bug 285746

Unfortunately, there is currently no way for system-cleaner to know which packages are obsolete (because they are no longer available via apt-get), and which ones are third-party packages installed outside of apt. Thus the bug is valid, but we can't fix it for now.

I discussed this with Michael Vogt. We'll work on changing libapt after intrepid to make this distinction possible in the future.