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.
You can then present them via javascript to allow filtering, searching, and tags.
https://github.com/skx/bookmarks.public