So I upgraded to OS X Mountain Lion yesterday. The install was pretty smooth (though had a tough time with the redeem code for the upgrade, worked on the third code that Apple sent across).
Most of the software is working fine. However, I found that my existing Xcode installation needed an upgrade (via a Xcode install from the App Store).
The problem is that any new Xcode install seems to nuke the command line development tools (think make, autoconf, etc.). The solution is pretty simple though. Once Xcode has been installed, run Xcode and then open the preferences. There is a section on downloads, which lists installing the command line tools as an option.
Voila! Issue resolved.