Using custom php.ini in a specific folder
In complement to @i_forget answer: You can use the php_admin_value & php_value & php_flag & php_admin_flag directives to alter specific settings on a Virtualhost or on a directory.
<Directory /path/to/foo> php_value include_path ".:/var/www/foo/lib:/usr/share/php5/apc" php_admin_flag file_uploads on php_admin_value upload_tmp_dir "/my/tmp/upload/"</Directory>php_admin_value is safer than php_value (idem for flag) as the application cannot use ini_set to alter the value.
Here's it's one a Directory tag, so it could be as well on a .htaccess but you should'nt use .htaccess files if you have access to the configuration, use AllowOverride None :-). It could be as well on the VirtualHost, so before the the Directory tag.