Q. When using a POP/IMAP Mail client, what protocol should be used in the configuration?
Although it is a user's preference, Google prefers mail clients be configured with an IMAP protocol. 

Q. Can I still use Outlook/Entourage/Thunderbird/ Mac Mail (or other clients) with GAE?
Yes, you can set up your client with an IMAP or POP connection. A brief description of the difference between POP and IMAP is available here. Basically IMAP is a two-way connection with the mail server and POP is a one way download of mail from the server. Instructions for setting up your client to use IMAP are available here. Instructions for setting up your client to use a POP connection are available here.

Q. Do we know if Google calendars populate POP mail calendars?
Google is capable of syncing with other applications.  Information can be found under calendar help – access options – sync.