Yes you can.
The way I'd do it is write your separate applications in PHP and Python, then upload them to the same application ID but name them as different versions. By uploading them to the same application ID, they can share common services such as task queues, paid settings, etc.
Note that versions can include letters and numbers, so you could call the application versions something like php1 and python1. If you need to communicate between each version, use task queues, the datastore, cloud SQL, etc. Or you can individually address each version using the appspot URL: http:// php-version . my-application-id . appspot . com (remove the spaces).