I like to keep my bookmarks local, even though it doesn't really make any sense, so bookmarking services like del.icio.us and such weren't on my mind at all. But I might look into those now, particularly for ephemeral bookmarks like links to specific articles and so on.
I did a 4 hour cleaning session yesterday (70% done) where I put my old bookmark folder structure inside a temporary folder, went through each bookmark, building up a new folder structure on the side as I went along, and either found a place for it or threw it out. I've recently done a similar thing with my physical stuff, going through everything and getting rid of stuff I've been hoarding for years. Must've thrown out, sold or given away 50% of my 'stuff' in the past year or so, and it was a very similar thing with the bookmarks.
Organizing them was easy when I figured out my reasons for wanting to visit the sites in the first place: ended up creating four top-level folders called Pers, Work, School and Temporary, and then a set of standardized sub-folders going from general->specific.
Thanks for the responses everyone, it feels good to de-clutter
