For reasons unknown to me, there’s enough functional change between PHP 5.2 and PHP 5.3 that it affected a lot of PHP-based programs. For that reason, PHP 5 in pkgsrc defaults to the 5.2 version. However, it’s going to be 5.3 for the next stable quarterly release of pkgsrc. In theory, all PHP5-dependent programs are ready to handle that now. Note that PHP 5.3 is already in pkgsrc; it just wasn’t the default. If you were using the php53 package, it may require some manual fiddling at your next upgrade of pkgsrc packages.