If you are comfortable with/living in vim anyway, you could give the vimwiki [0] plugin a try. You can use markdown as the markup language, which makes it easy to convert to whatever format you want to have using pandoc (or similar tools). Having the stuff in plain text lying around in a folder makes it very easy to search for using grep/ack.

This guy [1] describes how he's using vimwiki as a lab notebook (HN discussion here [2]). I used that as a reference for my own and I'm pretty happy with that for some months already and started to use it as a personal knowledge management system as well.

[0] https://github.com/vimwiki/vimwiki

[1] http://www.stochasticgeometry.ie/2012/11/23/vimwiki/

[2] https://news.ycombinator.com/item?id=4822796