People who like to mix bookmarks with notes and other free-form text might like a personal wiki. I've been using Tiddlywiki for this.

I'm also increasingly using a high-powered concept mapping tool for course design, business planning, and general information management: http://www.compendiuminstitute.org. It handles many types of information, including bookmarks--you just drag the favicon or URL into the Compendium map and the site is added to the map. The result is a visual map of websites, Word docs, PDFs, notes, and other information.