You can use Bookmarks Tags to organize bookmarks with categories, not folders.

Bookmark Tags allows you to easily organize your bookmarks. Instead of deciding on the one, appropriate folder to place a bookmark in, you assign it any number of "tags," or categories, and let Bookmark Tags organize your bookmarks for you. And with the tag browser sidebar and window, instead of hunting for bookmarks through hierarchical folders and subfolders, you can browse with tags, using your categories like a sieve to filter out unwanted bookmarks.

When you tag a bookmark, by default Bookmark Tags automatically organizes your bookmarks tree by creating folders that correspond to the tags -- one folder for each tag, with all the bookmarks tagged by a tag under the corresponding folder. But Bookmark Tags is flexible. You can customize it so that as many paths to a bookmark are created as there are permutations of its tags. Or if none of that suits you, you can turn off automatic organization altogether and pick folders yourself, like usual.

This extension was developed for two reasons: to bring local (anti-social?) bookmark tagging to Firefox, and to organize tagged bookmarks within the bookmarks hierarchy in a way that makes sense. Bookmark Tags 0.2 introduces the tag browser window and sidebar, which allow browsing by tags outside of the hierarchical bookmarks tree.

You can download the extension from here.