[ideologysec]

TreeStyleTabs in Firefox (which is a great tool regardless of bookmarking), keeps track of parent/child relationships, you can drag & drop into subsets to create the relationship you're talking about, and has a "Bookmark this tree" feature, which would create a folder with subfolders with the top level named as you choose.

(I use the heck out of this, both for the extra vertical space that comes from hiding the top tab bar, and for the conceptual organization that it provides).