I think i know what you mean now. You want a js file to be sent to the client, but you want to process it as PHP so you can modify the js file before sending it to the client.
If so, try:
<Directory /var/www/somespecialjsfolder >
AddType application/x-httpd-php .js
</Directory>
You'll probably need to add PHP code to set mime-type to application/x-javascript on output of your js.
That said, this is probably a bad idea. You don't want to have to debug Javascript which is different for every client. Put all your client customizations in the js file, keep it consistent. Abstract things out with JQuery or equivalent.