How do I restore autoconf after Mountain Lion update?
It sounds like you're a developer. You should install Mac Ports. It's REALLY helpful and useful to have. You can use it to get command line tools such as autoconf. It's always useful to have if you work with command line a lot.

Just install the .pkg from http://www.macports.org/install.php to install MacPorts.

After so, in terminal, run:
sudo port install autoconf

More info:
http://www.macports.org/ports.php?by=library&amp;substr=autoconf