brew uses /usr/bin/autom4te in stead of /usr/local/bin/autom4te
I went ahead and renamed the files autoconf, autoheader, autom4te, autoreconf, autoscan, autoupdate and ifnames in /usr/bin to force my machine to use the ones made available in /usr/local/bin after a brew link --force autoconf.

Brewing worked without an issue.

I don't know where the files in /usr/bin/ came from or if I borked things up bad by doing this. I'm keeping the renamed files in place, just in case I ever remember what I did today when things start to stink.

(see https://github.com/mxcl/homebrew/issues/20586 for more troubleshooting)