The trick is to manually set the correct paths and then run configure inside the virtualenv. This is quite basic, but it worked for me.
Install python-config in the virtual env and link it to python2.7-config:
pip install config
ln -s /home/PATH/TO/VIRT/bin/python-config /home/PATH/TO/VIRT/bin/python2.7-config
Install cairo in the virtual env:
wget http://cairographics.org/releases/py2cairo-1.10.0.tar.bz2
tar -xf py2cairo-1.10.0.tar.bz2
cd py2cairo-1.10.0
./waf configure --prefix=/home/PATH/TO/VIRT/
./waf build
./waf install
Install PyGTK
wget http://pypi.python.org/packages/source/P/PyGTK/pygtk-2.24.0.tar.bz2
tar -xf pygtk-2.24.0.tar.bz2
cd pygtk-2.24.0
export PKG_CONFIG_PATH=/home/PATH/TO/VIRT/lib/pkgconfig
./configure --prefix=/home/PATH/TO/VIRT/
make
make install
And that should do it. Just replace PATH/TO/VIRT/ with your own path. I’m sure someone could assist on adding the path to virtualenvwrapper?