I was reading Ask HN: How do you organize your text files?, and I noticed Vimwiki mentioned by gregmorton. Sometimes writing anything in something that isn't Vim (Evernote, OneOne, etc.) feels awkward, but directories full of text files are hard to manage. That's where Vimwiki comes in.
Vimwiki adds syntax highlighting for a text-based wiki language that allows you to organise notes and to-do lists. If you press enter over a word you can create a vimwiki page. It seems like a good alternative to a mess of text files!