[Editor's note: The reason why some general options for the "configure" scripts are not documented is that said script is part of the GNU autoconf tools, and as such its general options are documented elsewhere, e.g.: http://www.gnu.org/manual/autoconf/index.html and http://www.airs.com/ian/configure/. Some are also documented in the INSTALL file that comes with the source distribution.]
The --prefix=PREFIX configure option isn't mentioned here. It apparently defaults to /usr/local, and sets the position of the php includes and libs. (in PREFIX/include/php and PREFIX/lib/php)