Most browsers let you create folders on the bookmarks toolbar. I've been trying to sort the bookmarks I use most often into different categories to make finding them easier. Here's how they're organised so far:
sites: the sites that I maintain - links to front pages and admin pages.
local: services running on the local computer (notebook, wiki, phpmyadmin, etc).
accounts: sites with a personal account (del.icio.us home, webjay playlists, flickr photos, google search history, my yahoo!, etc).
incoming: pages that are checked quite often (del.ici.ous inbox, flickr photos from contacts, tracks from last.fm friends, torrent feed aggregator, latest news). It might be useful to have a dashboard page that shows all these at a glance. Mailing lists should probably be here as well (showing latest conversations)?
keep: pages accessed sometimes, when looking for something to read, that don't churn quickly (del.icio.us popular, hot links, software updates, link filters, flickr explore, popular torrent charts, radio players).
bookmarklets (but not for search - those are all moved to search plugins).
comments: sites to revisit to check on comments left (might work well as live bookmarks, to check automatically for changes - need to remember to unsubscribe though).