Unless you want the last version of numpy or scipy, you should use the version available in your distribution:

apt-get install python-numpy python-scipy

If you really need to build from sources, you need the following packages on Ubuntu (8.10 and above), and on Debian Sarge and above:

apt-get install python-dev libatlas-base-dev python-nose

You can then build both numpy and scipy as follows, inside their respective source tree:

python setup.py build_ext --fcompiler=gnu95 install --prefix=where_to_install_numpy

Those instructions work without editing the site.cfg.