Две версии php, как?

<VirtualHost 8.8.8.8:8080>

   AssignUserID admin admin

   ServerName site.com

   ServerAlias site.com

   ServerAdmin info@site.com

   DocumentRoot /home/admin/web/site.com/public_html

   ScriptAlias /cgi-bin/ /home/admin/web/site.com/cgi-bin/

   Alias /vstats/ /home/admin/web/site.com/stats/

   Alias /error/ /home/admin/web/site.com/document_errors/

   #SuexecUserGroup admin admin

   CustomLog /var/log/apache2/domains/site.com.bytes bytes

   CustomLog /var/log/apache2/domains/site.com.log combined

   ErrorLog /var/log/apache2/domains/site.com.error.log

  <Directory /home/admin/web/site.com/cgi-bin>

        AllowOverride All

         Options +Includes -Indexes +ExecCGI +FollowSymlinks

</Directory>

 <Directory /home/admin/web/site.com/stats>

      AllowOverride All

</Directory>

#Include /home/admin/conf/web/apache2.site.com.conf* <--- а тут что ?

</VirtualHost> 

AddHandler php-cgi .php .php3 .php4 .php5 .phtml

ну и симлинк вашего cgi сделайте в /home/admin/web/site.com/cgi-bin:

ln -s /opt/php5.2/bin/php-cgi  /home/admin/web/site.com/cgi-bin

вроде бы так.