If a module SAPI is chosen during configure, such as apxs, or the --disable-cgi option is used, the CLI is copied to {PREFIX}/bin/php during make install otherwise the CGI is placed there.
versus
Changed CGI install target to php-cgi and 'make install' to install CLI when CGI is selected. (changelog for 5.2.3)
http://www.php.net/ChangeLog-5.php#5.2.3