Is there a way I can have multiple ssl certificates point to a single inputendpoint in a service definition? For example, lets say I have two url\'s.
service.foo.ne
"Oliver Bock"'s answer may work for you and "Igor Dvorkin"'s answer is not valid anymore since IIS 8 with Windows Server 2012 supports SNI, which enables you to add a "hostheader" to HTTPS bindings and having multiple SSL certificates to different domains listening to the same HTTPS port.
You need to automate the process of installing the certificates on the machine and add HTTPS bindings to IIS.
I'm a Microsoft Technical Evangelist and I have posted a detailed explanation and a sample "plug & play" source-code at: http://www.vic.ms/microsoft/windows-azure/multiples-ssl-certificates-on-windows-azure-cloud-services/