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 target by mistake.

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