Finally cPanel have modified the exim config which allows you to send the emails of individual domains from the IP assigned them and not the primary IP of the server! This is on cPanel release 11.23.
The setting to enable this can be found in WHM under exim configuration. What you can do is then assign each domain to an IP (if you have enough available) and then the email will be sent from that IP. Make sure you remember to set up rDNS on that IP though!
Hopefully this will help get round yahoo sending emails to junk automatically because it's a shared IP!
You can get more info about the upgrade here:
cPanel 11.23 RELEASE Announcement cPanel Blog