I have two webapps WebApp1 and WebApp2 in two different domains.
Do what Google is doing. Create a PHP file that sets the cookie on all 3 domains. Then on the domain where the theme is going to set, create a HTML file that would load the PHP file that sets cookie on the other 2 domains. Example:
Please wait.....
Then add an onload callback on body tag. The document will only load when the images completely load that is when cookies are set on the other 2 domains. Onload Callback :
setcookie.php
We set the cookies on the other domains using a PHP file like this :
Now cookies are set on the three domains.