I use Gitit [1] as my personal wiki for notetaking. I've been pretty happy with it so far, as it uses the excellent Pandoc as the backend. I have not heard of Vimwiki until now - can you tell me your favourite features?
* plain text edited in vim ;-)
* links (to other wiki pages and content), move cursor over link and <Enter> will open wiki page, link in browser, image in image viewer, pdf in ... all from your console
* manages todo lists (including status indicator auto update for sublists: [.]->[o]->[O]->[X])
* headers (mostly useful when exporting to html)
* table creation and management
Overall a very lightweight and tightly integrated vim plugin, but gitit looks quite interesting, might give it a try.