For what it's worth I had the same problem with folder/hierarchically structured bookmarks, but tag-based bookmarking (like del.icio.us used to provide) meshed

For what it's worth I had the same problem with folder/hierarchically structured bookmarks, but tag-based bookmarking (like del.icio.us used to provide) meshed very well with me and my workflow so I wrote https://savecrate.com https://savecrate.com (still a WIP and rough around the edges but functional enough to work for me)