Can I clear out broken/uninstalled apps that still show up in the app list? I had some apps stored on my SD card that I have since wiped. The apps still show up in my app list in Settings->Manage applications. How do I refresh this list?

Rebooting the phone doesn't help, and clicking on one of the entries causes the Settings app to crash. I even tried wiping the Dalvik Cache, but the missing apps are still listed.

One special thing to note is that I had used Link2SD to link the apps onto a second partition on the SD card. This is different from the built-in Android method of moving to the sd card. Link2SD creates symlinks so that any app can be moved, and the SD card can be mounted on a computer without temporarily disabling the app (because they are on a second, unmounted partition). I don't know if using Link2SD changes my situation.

Note that these uninstalled apps do not show up in another application's app list, such as Titanium Backup.
I also had this issue.

I found that if I use link2sd to uninstall the app, it should remove the entry from the app manager.