I use vimwiki! It has a markdown mode (which I use) in addition to the default wiki markup mode.
I've built a personal organization system on top of it that consists of:
What I love about the wiki format is that I can treat my organization system as a graph (I mean, it's a wiki after all). I link to work item pages from my daily logs if I have relevant thoughts about them, or meetings.
Some day I might make this thing start automatically exporting HTML but for now I'm content to browse it just within vim.
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