Just my 2¢: I'm also using plain text files as a 'mind-dump'/exocortex/organsation system. After a while, the file tends to get rather big, and so I need some coarse hierarchical levels, like 'random cool stuff to look at when idle', 'high priority stuff/this week', 'medium priority stuff/this month', etc. A copious amount of unicode and especially ASCII art helps me a lot to find sections quickly. Behold my elite retro headers like
Markdown-style headers (with - or = underlines) also help a lot to organise within the top-level sections. In general I find it very helpful to re-use Markdown (or reStructuredText) syntax, even if it's not rendered.
