We have just spent a great deal of time head down writing documentation on all sorts of SharePoint protocols. They are split into two groups Front End and Back End. Front end protocols are all the ones that typically talk to a front end web server and the back end ones are mostly how the front end server talks to other servers such as SQL Server.
So if you ever wondered what how a particular SharePoint protocol worked ... now you can read all about it.
Grab them here: SharePoint Products and Technologies Protocols