For our e-commerce service running on AppEngine we would like to offer the option for customers to run the stores on their custom domains (eg: www.mystore.com instead of www
Another option is to have each customer sign up for google apps, and then add your appengine app to their app. That way they can manage the url. They will need to use a cname for this, so urls will be limited to something like 'store.customer.com' You will have to support the multitenancy off of the host-header, but that isn't hard to do given that you already have a way to support multitenancy already. You might want to do the setup for the first couple of clients yourself so you can document the easiest way to set it up.
The rietveld code review app does this as you can add it to your google apps domain. See http://code.google.com/p/rietveld/wiki/CodeReviewHelp#Using_Code_Reviews_with_Google_Apps for more detail.
The preferred option is probably to offer your solution through the Google Solutions Marketplace: http://www.google.com/enterprise/enterprise_marketplace/about.html