If you're hacking configure.in (any of them), the following guidelines should be followed.
All help strings should use the AS_HELP_STRING macro.
All *nix (and windows if it works there?) dependencies should use pkg-config to detect whether they exist or not.
Be careful about making dependencies build automatically. See http://www.gentoo.org/proj/en/qa/automagic.xml for why automagic dependencies are bad. The problem is that developers by default will want all options enabled, while packagers will only want options enabled if they are specifically asked for.