- org-mode or text files in general make it easy to add contextual information, additional notes etc. Bookmarks can finally tell a story.
- in org-mode (or Markdown), the bookmark file is well-readable as is in the editor
- bookmarks can be rearranged and regrouped quickly if need be
- (org-mode at least makes) links to different sections of bookmarks within the same file possible. For this reason, I personally don't use tags but follow a hierarchical structure with intra-document references if need be (e.g. if a group of bookmarks can be considered to be part of two different higher-level groups)
- searching is only one grep or one Ctrl+F away. In case of imprecise search terms, the additional hierarchical structure helps.
- Easy and privacy-preserving synchronization among devices using git
And here are the disadvantages:
- No browser integration; bookmarks always have to be added and looked up manually which is particularly cumbersome on a phone.