"Once the source grows beyond 1000 words or so, it can all too easily
become disorganised, and by the time it reaches the size of a novella
it can be difficult to find things."

The documentation then advocates the use of headings to organise
source code.

Can anyone point me at an exemplar which shows good use of headings
for source code organisation?

MTIA

Regards,
Peter

http://inform7.com/learn/complete-examples/

They were written by the developers of Inform 7 and should be reasonably  
good exemplars of how to organize code. Ultimately, this will be a largely  
personal thing anyway, but these are probably a great place to start.

If you're wanting to write extensions, then code organization becomes a  
bit of a different beast, because you should also take into account the  
ease with which others can modify your code (e.g., by replacing bits they  
need to change), as well as laying it out logically for consumption by  
others. I think Michael Callaghan, for one, does a marvelous job of  
arranging extensions in a way that is easy to both digest and to hack  
around with.