My experience matches majo's. With my apache 2.2x, I could not set separate php.ini files for each site, even using httpd.conf.

However, it may be possible to set specific php variables on a per-site basis if you have access to httpd.conf.

I was able to set some php_value variables in .htaccess, but php_admin_value variables, such as "sendmail_path" must be set in httpd.conf. My only goal was to use separate msmtp accounts to send through Google Apps from different sites. 

 I did this by putting the following inside the root directory <Directory> tags for each site: 

 php_admin_value sendmail_path "/usr/bin/msmtp -C /path/to/msmtprc -t"

 For example: 

<Directory "/var/www/site1">

  php_admin_value sendmail_path "/usr/bin/msmtp -C /path/to/site1msmtprc -t"

</Directory> 

 <Directory "/var/www/site2">

 php_admin_value sendmail_path "/usr/bin/msmtp -C /path/to/site2msmtprc -t"

 </Directory>

In my case, I have separate conf files for each site, and I placed these strings inside each conf file between the <VirtualHost> tags. I am not sure if these commands would work outside of a virtual hosting situation, but it may be worth a try.  

 I know this is a bit off-topic, but I found this site looking for the information that I have written here; hopefully this may help someone else.