Well I hesitate to recommend it for use by others, but what I use is my home-grown zknotes. Markdown notes that you can link together, so any note can be a tag. There's a query syntax that allows searching note titles or content or tags. Notes live in a sqlite database. You can upload binary files like movies or images. Currently working on synchronization between instances, that will enable a phone app that syncs with a home server. If you run a server with it you can make documents public as a blog.
Downsides: the interface is a bit kludgy, and probably won't improve until I'm done with sync and the app. No cli interface for searching or export. No code highlighting yet. Not many users so the multi user capabilities are mostly untested.