DokuWiki

I like DokuWiki for its simplicity and extensibility. All articles are stored in files, and the structure is maintained by a directory tree. It runs with very few requirements (PHP is one).

Since I'm familiar with the CLI, I can manipulate articles fairly easily, and have even imported a series of articles by simply copying from one machine to another.

The markup language is fairly straight forward, and you can use pandoc to convert from a different markup language (like Markdown) quite easily.