Just a lot of tags. I've got 457 tags at the moment.
Then of the question becomes how to manage all those tags, and I use a Usenet-like system of hierarchical tags. The tag about the PHP programming language, for example, is comp.lang.php, whereas the tag about nuclear physics is sci.physics.nuclear. I also have a lot of tags under the misc.* hierarchy, just like in Usenet. So I get the best of both worlds: the flexibility of tags and the organizational neatness of folders/subfolders.
The only drawback is that Pinboard won't let me search by a prefix of the tag, like sci.physics.* to get all physics articles. Bundles might help, but I'd have to create and manage them manually so I haven't bothered. If I really need to run a complicated search, I'll just dump all my bookmarks and process them locally.