Bookmarks not saved
This article deals with problems adding, deleting, and making changes to bookmarks. For bookmarks that were saved previously but are now gone, see lost bookmarks.
Changes lost on restart
This problem can be caused by a read-only bookmarks.html or bookmarks.html.moztmp file in the profile folder. In this case, deleting or modifying bookmarks will also have no effect and the profile folder will fill up with multiple numbered bookmarks-n.html files. Removing the read-only attribute will again allow the bookmarks to be updated. [1]
Add Bookmark dialog doesn't work
A corrupted localstore.rdf file in your profile folder can cause this problem. The solutions below will fix it, but you will lose and toolbar customizations you might have [2]
Firefox 1.5
Close Firefox and start it in safe mode. Select "Reset toolbars and controls" and choose "Make Changes and Restart"
Everything else
With the application closed, open your profile folder and delete localstore.rdf.