Hmm, almost never actually. The only example I can think of is PIL. I usually have to manually edit the installer to get libjpeg and zlib and fooimagelib to install properly. Other than that, pip seems to have all the magic I crave.
(assuming you have the relevant libjpeg-dev etc already installed)
There's distutils which was the original one and is part of the standard library, setuptools which extends distutils and adds some very useful things like dependencies, then distribute split off from setuptools because of a number of reasons. Just recently distribute merged back into mainline setuptools and the distribute project is now done and it's maintainers have taken over setuptools.
In the middle there was also distutils2/packaging which were attempts at replacing the entire thing but have since been abandoned for a number of reasons such as trying to replace the entire toolchain at once.