For my bookmarks, I got lazy and now just use Firefox/TenFourFox/Iceweasel with a local sync server. So, I use Firefox's system, which allows for hierarchical and tag-based organization, and searching based on title. Prior to that, I used Delicious, which also had tags, and searching.

I can't speak for anyone else, but these days I use bookmarking as a contingency, in case I remember later and need or want the link to whatever. So, I'll bookmark just about anything and everything I might possibly remember, regardless of real value or intention. In the past, I used bookmarks to represent an active intention to go back and follow up on whatever, so I would carefully curate and organize my collection.

Your project seems like it would be very useful for the latter. And these days, for me, the latter comes up most often when I also intend to share the collection with others. For example, sharing a set of bookmarks to websites covering candidates or ballot issues in a local election.