In general no, but in special (CGI/FastCGI) yes: http://php.net/configuration.file.per-user
Since PHP 5.3.0, PHP includes support for .htaccess-style INI files on a per-directory basis. These files are processed only by the CGI/FastCGI SAPI. This functionality obsoletes the PECL htscanner extension. If you are using Apache, use .htaccess files for the same effect.
In addition to the main php.ini file, PHP scans for INI files in each directory, starting with the directory of the requested PHP file, and working its way up to the current document root (as set in $_SERVER['DOCUMENT_ROOT']). In case the PHP file is outside the document root, only its directory is scanned.
You can only set a limited subset of the ini-options in the user-ini-file. If you are hosting several independent sites on one server, you should consider FastCGI anyway, to keep them separated. With php5-fpm
it's very easy to setup many pools of workers.