In the past I used Soywiki, which, like Vimwiki, is a wiki inside Vim. While I love Vim, it was too inefficient to have to ssh into a box, cd into ~/wiki, and launch Vim just to read or edit an entry -- especially on my phone.
The solution I've found is called Gitit, which stores entries as plaintext in Git like Vimwiki and Soywiki, but adds several additional features on top of that:
- powered by Pandoc, which means you can write entries in Markdown/LaTeX/reStructuredText/Literate Haskell, and export them in almost any format, including PDF, HTML, LaTeX, Markdown, ePub, and ODT.
- a customizable web interface. I used Bootstrap to make the wiki look great everywhere. Couple that with the speech-to-text features in Android 4.0+ and storing your knowledge becomes effortless anywhere.
- a Haskell plugin system. You can write plugins with access to the Pandoc AST, allowing you to do things like archive all outbound URLs or enable [Interwiki](!Wikipedia) links.