+1 for hierarchical tags. I've been organizing all my bookmarks (about 12K going back more than a decade) with Usenet-style tags like comp.lang.python and sci.bio.paleontology for several years now. It works great, especially since Pinboard lets me autocomplete by tag prefix.

One of the things that I think most services like Gmail missed when they tried to replace folders with tags is that although the same item can belong to multiple categories, the categories themselves usually don't have a completely flat relationship to one another. An article can relate to both Python and paleontology, but that doesn't change the fact that Python is a programming language and paleontology is a subfield of the biological sciences. This will be very useful later when I'm trying to remember something that uses some programming language to analyze data in some subfield of the biological sciences, for example.

Tags look cute on a screenshot when you have a few hundred items. But when you have tens of thousands of items, you need a bit of hierarchy to protect your sanity.