How do I know when what I should store in my external to /etc configurations in etckeeper?

I read about the ability to store configuration files that live outside of /etc here, and I tested it out on a test server, and it appears to work. One thing that I'm having a bit of an issue with however, is identifying what of these files external to /etc in an application needs to be included and what needs to be left out. What makes a file a good candidate for inclusion or exclusion in etckeeper? It seems to me that if you have an application that sits at the top of a LAMP or other stack, that it's configuration file and .htaccess or equivalent should be included in /etc to have a log of changes that can be included in the same commit. While I know you could conceivably store the entire application in git, it slows down commits, and mis-uses git. It also seems that anything considered cache or binary should be excluded, but that any text-based configuration files should be included.