Which is best?

There is no panacea, of course. Each solution has its merits and drawbacks.

You cannot use BUILT_SOURCES if the ability to run ‘make foo’ on a clean tree is important to you.

You won't add explicit dependencies if you are leery of overriding an Automake rule by mistake.

Building files from ‘./configure’ is not always possible, neither is converting ‘.h’ files into ‘.c’ files.