Update: In BeOS 5, you can configure the GoTo menu much like you configure the Deskbar, with a nice GUI panel. In any file panel, pull down Favorites | Configure Favorites. The old tip still works, so it remains below.

Another tip explained how to add items to the GoTo menu in open/save panels. Now, how to get rid of them?
The GoTo menu items are stored as links in the folder ~/config/settings/Tracker/Go/. You can add or remove links inside this folder.