I built a web application for managing lots of bookmarks. It's up over at linkzie.com. The original idea came from a little python script I built way back in 2004 that would generate a page similar to linkzie, albeit a very crude version initially. All the data was manually edited into the script by hand and then the script could regenerate a new HTML page. Linkzie has now been made into a modern multi-user web application with easy drag-n-drop organization and a nice single page application AJAX user experience. There's more information on the Linkzie site, so please go check it out.