There are 2 main protocols or items used here for either the retrieval or delivery of e-mail.
The first one is called Simple Mail Transfer Protocol (or SMTP for short), which is the Internet's standard host-to-host mail transport protocol. Simply put, SMTP is what allow for the sending of your email, either when using your ISP or using the servers here (mail.yoursite.com).
The second is called Version 3 of the Post Office Protocol (or POP-3 for short), which is designed for user-to-mailbox access. Simply put, POP-3 is what allow for the receiving of your email, either when using your ISP or using the servers here (mail.yoursite.com).
These are the main protocols used today in most Computer-based email programs such as Outlook or Eudora and many others.