Missing autoconf/automake in Xcode 4.3?
For what it is worth- (and others stumbling onto this problem like I did) in the latest XCode (4.6, 4.5 and friends) autoconf is not even available in the command line tools. 

I have manually installed just autoconf and a few friends, but still have trouble with some of the automake-ish software out there. 

See http://jsdelfino.blogspot.com/2012/08/autoconf-and-automake-on-mac-os-x.html for a how-to to manually install.