Especially Bookie looks good and would be a preferred candidate to transition to if you are still using the very old 'Sitebar', 'Scuttle' or the interesting 'Semantic Scuttle'.
Well, a note-taking solution (be it a plaintext file or a simple database) can perfectly handle the task of keeping URLs, but I think the point of bookmarking service are social aspects and/or content archival and indexing. Otherwise there's no reason to just not stick to what browsers have built-in for ages.
Sadly, Bookie seems to be somewhat dated and not actively maintained. I've thought of trying it out, and now have hard time packaging it.
By default, it won't even start on modern distributions because of incompatibility with Python >=2.7.11 ("cannot import name _uuid_generate_random"). The requirements.txt file require a few version bumps. I haven't tested whenever the project actually works correctly with those yet, but it seems to at least start with kombu==3.0.35, celery==3.1.23, billiard==3.3.0.23, amqp==2.0.2, redis==2.10.5.
(I'm lazily toying with it remotely, setting it up on a small ARMv7 host, wrapping it with Docker+honcho+gunicorn, and rebuilding the image when I update requirements takes long time...)
You can then present them via javascript to allow filtering, searching, and tags.
https://github.com/skx/bookmarks.public