I've used the file name technique.
It worked great, until I decided to archive anyting that hadn't been modified
for in the past year. It got archived.
Then, when the application  quit working, I had to revist a program that I hadn't
had to touch for over a year in order to find out what happened.

so I changed the name of the file to: DO_NOT_DELETE.txt
then, I was sure to put some comments describing what it was for.

It's not perfect, but I haven't archived it again either.