I was just thinking about this at the weekend. One approach is to use a tool that supports [[Wiki-style Linking]], and have a kind of index/table of contents/home page for your notes.
That's what I do today in my own app. I have a "table of contents" file in each folder. Ideally the file system would support that out of the box, but maybe a first step could be to standardize such a TOC file...?
