I upgraded my macbook to Mountain Lion today and found that I no longer have autoconf installed, is there a specific way to restore that or will I need to manually compile it etc? I have XCode 4.4 installed with Command Line Utilities downloaded and installed as well. Thanks for the information!
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
If you already have the latest XCode installed go to it's Preferences -> Downloads pane.
You can install the Command Line Tools there. You may need to reinstall Xcode and then install the Command Line Tools in the same way if that doesn't work.
Either way, to solve this specific issue you don't 'need' Mac Ports as it is a known issue that can be solved as above.