What I would like to see is tags used instead of folders - so that you can combine them with union and intersection (particularily intersection) integrated with sort and search by words.

In fact I have a prototype bookmarking app where I put some of my ideas for an ideal user interface for an archive: LinkMine

• recursive search - the presented list can be searched and filtered just like the whole archive.
• clicking on properties (like tags, host, author) adds this property to the filter - together with the previous point it makes a very effective and integrated interface for searching and browsing.
• in the right panel you have a list of all tags (tag cloud) used on the current result (this panel is paged - this might be not clear) - this let's us to treat the tags as if they were folders. This can also be generalized to a faceted interface for all properties, but it might be heavy on server resources.
• bulk operations on whole pages of bookmarks (this is not yet fully implemented)

This is a Catalyst web application and I can give you the source code. At Tags and search and DBIx::Class I've described my DBIx::Class database model supporting this interface.