The thing that bothers me about any kind of service that keeps a copy of your bookmarks remotely is privacy.
Say Obamaniacs want to single out pro-lifers for harassment. My bookmarks would be a happy hunting ground. Speaking of hunting grounds, they’d find a few pro-gun sites in my bookmarks as well.
Maybe the remote backup is optional with Foxmarks; I don’t know.
By default, and the easiest way, it uses the Foxmarks server. But, as explained at Using Other Servers, you can use your own web server, so long as it supports FTP or WebDAV. I use Fastmail.fm for email service, and they provide WebDAV services, which I use to synchronize my Firefox bookmarks via Foxmarks.