I have been wanting this for so long. The idea is similar to what is already implemented in evernote's system, where you can copy a link to one of your notes and paste it into your other note, so when you click the link, it sends you over to the other note you have.
The system I am looking for is -within- a note itself, however. Perhaps a "pop-up" bar on the left / right side of the note would give you an overview of all of your 'bookmarks' / 'titles', etc. so that way you can make really intense and long notes with many different subjects / topics within them, and still have a very easy overview and a way to switch between your most important topics.
I hope this makes sense; it's similar to what you can do in word as well, where a Title format will allow you to view all of your headers on the side of your document for easy access.