Due to security restrictions it is super easy only if the parent window and the popup are from the same domain. If that is the case just use this:
// Store the return of the `open` command in a variable
var newWindow = window.open('http://www.mydomain.com');
// Access it using its variable
newWindow.my_special_setting = "Hello World";
In the child (popup) window, you could access that variable like this:
window.my_special_setting
Was there something specific you wanted to do past that?