If you want to see the patches go into the Debian/Ubuntu packages, run apt-get source php5 and look at the php5-$version/debian/patches directory. The build process uses a quilt wrapper (dh_quilt_patch) to apply them in the correct order. There are patches for building (in general or for a specific architecture), segmentation faults, security issues, manual pages and very few configuration changes (mostly just FHS compliance).