[dimatura]

I use mainly two tools: The vim notes plugin (https://github.com/xolox/vim-notes) and zim wiki (http://zim-wiki.org).

vim notes is very good at quickly jotting down and bringing up things from vim; much better than vim-wiki, in my experience. While it can export to html, since the main interface is vim it is not that nice for embedding images and such. Therefore I use vim notes mostly for stuff related to coding, which is naturally text-friendly.

For research notes and results, I've been using zim-wiki. While it has a GUI, it is a text-based format. Whenever I feel the need for vim shortcuts I just open the page in an external editor (vim), which is even supported in the GUI. The markup is not markdown but something similar to mediawiki, which is annoying but not a deal breaker. It can embed images, tables and latex equations (though the UI for this could be better; instead of a directly using $$ in the markup, there's a dialog). Since you mention screenshots, it also has a "embed screenshot" plugin which I've been using a lot more than I thought I would. It's also open source and has what seems like a healthy community.