The following is my list of ports and protocols for SharePoint communications between servers based on my experience. Many are optional and rely on how your network is set up. The items can be configured with custom ports.
WFE = Web Front End
APP = App server
Search = Search server
UP = User Profile
AD DS = Active Directory Domain Service
BDC = Business Data Connectivity
Sorry for the image... it was difficult to fit the table on this page, so an image was the best choice I had to be compatible across devices.