From this question I learned that Google App Engine does not currently support SSL on \"custom domains\" (at least not as of June 2010, when that question was asked).
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You can get SSL to work on your custom domain hosted on AppEngine, however you need to run a reverse proxy that can modify the host header to do so. If you want to setup a reverse proxy yourself, you can do so following these instructions:
http://radomirml.com/2011/01/30/reverse-proxy-for-gae-application-using-nginx-and-ssl
Alternatively, you can use a reverse proxy service like CloudFlare. The process of getting SSL to work with an appspot.com domain is documented on the CloudFlare Blog:
http://blog.cloudflare.com/ssl-on-custom-domains-for-appengine-and-other