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.
I guess you could automate that if you really wanted. Another idea would be to put your vimwiki folder into your Dropbox.
As vimwiki files are plain text you can really do almost anything to them.