how can I reorganise 1000's of bookmarks?

my bookmarks number about 3000, with about 30+ category folders.

lists and lists of boomarks! i'm looking at the following:

a bookmarks manager app called webbla- doesn't seem to offer much different

using the 'reader'- which i find excellent

thinking of moving the lot to an external flash drive, except favourites.

any support users' experiences or novel ideas welcome!