The GTD additions to my bookmarks: On the toolbar, I have two folders: "To Be Processed", and "ACT". I drag links into the first while working so that I can consider them while processing. In the second, I put links related to actions on my action lists. I don't use links in "ACT" as action reminders, though; they could be thought as action support.
Otherwise I treat bookmarks as reference, and follow my intuition for creating folders and subfolders. It is not much different from my pre-GTD days, except that it is more dynamic: I prune irrelevant ones more often, and I can create per project folders, which can go away when the project is done.
Regards,
Abhay