You basically have to use the corresponding versions of either
pip. Unless you installed
pip in the Apple-supplied Python, it will only work with the 2.7 version (assuming you installed it there), so you must use
easy_install. Try doing
sudo /usr/bin/easy_install shapely, which will install shapely using the
easy_install located in /usr/bin/.
Now, if you have updated your OS X to Lion or Mountain Lion, the Apple-supplied Python will be some earlier version of 2.7. Try uninstalling QGIS and then installing it again. I read somewhere that QGIS will recognize both 2.6 and 2.7 Apple-supplied Python versions.