You should consider App Engine's native support of multitenancy. If this is not good enough for your requirements, then you will have to create a separate project for each customer. The Datastore for a single project is shared across all versions, so you will not be able to segment it (unless you are ok using namespaces as described in the linked doc).
I would also recommend making sure that you actually need to have separate applications running for each customer. Unless you sign up for a premier account, you have a limited number of projects that you can create. Besides that, it will most likely make management of those apps much more difficult for you.