I run a bookmark manager on my home web server (accessible from the internet). I prefer that over managing bookmarks using browser facilities, because I can use bookmarks from any browser and any machine, anywhere. I also don't have to worry about losing bookmarks if I change browsers, replace the OS, etc.

I'm also a bit allergic to using some external service to do this -- that seems like a pointless loss of control to me.

(I use Online Bookmarks http://www.frech.ch/online-bookmarks/ for this)