That's where Bookit comes in handy. There's three options: Manage, Migrate or Restore. You can manually edit bookmarks, and compare them to a 'master' set (in my case, Camino); Migrate will allow you to take a browser's bookmarks, and completely over-write existing bookmarks on any other browser (or overwrite a synchronised copy of your Bookit bookmarks on .Mac), while Restore will allow you to retrieve a previous configuration. With only Safari able to synchronise bookmarks via .Mac, the ability to do so with Camino and Firefox is a welcome relief for those of use who don't (always) use the default OS X browser.
I've used Bookit on three of my Macs around the home and office, with the application working perfectly in bringing my bookmarks across to all of them. Given that the application costs just $12, if you're working with multiple browsers, favourites and machines, I'd highly recommend Bookit.