Since that thread has just been revived, let me just mention, in case someone is interested, that I found a rather good (free) note-taking program which can be used as a standalone bookmarks manager.
It's Tree Line, and although its website has a sort of Windows 3.1 look, it seems to be actively developed. The program is simple, clean and straightforward. It needs a bit of tinkering for the database to be adapted to one's use, but there are several ready-made templates, and Bookmarks is one of them. It has all the main features I always wanted from Firefox, but Mozilla never cared to provide.
It does have an irritating issue though : when trying to type or paste contents into a field, that content would often jump to the next field instead... And there's only a mailing list for support, no forum.
Another, dedicated desktop bookmarks manager I found is Rons Web Lynx. It's in the early stages, I find the interface a bit noisy and childish, but the developer seems energetic and deserves to be followed.