Overview
Email is handled by various protocols. While all of these are designed to deliver your e-mail to you, there are some fundamental differences. On servers where you have a choice between different delivery protocols, you will need to choose the protocol most suited to your situation.
IMAP
IMAP stands for Internet Message Access Protocol (formerly known as Internet Mail Access Protocol). The most distinctive feature of IMAP is the fact that your e-mail messages remain on the server, instead of being downloaded to your computer. This is advantageous if you access your e-mail from multiple devices (such as a computer and a smartphone), or if you expect to require access to your e-mail a web browser. Checking your e-mail with a client or web-based environment using this protocol will allow you to retain your messages in a universally-accessible place for access whenever and wherever you need them. IMAP supports the use of folders for mail organization, but instead of organizing the messages on your local computer, these folders are kept on the server as well. Another advantage to IMAP is quicker access to e-mail. If you access your e-mail from a slower connection, such as modem dial-up, you will notice a substantial increase in speed; only the message headers are initially downloaded, so you can choose to download, open, and read only those messages of interest to you at that time. One drawback to using IMAP and saving messages on the server is that you will be restricted by any quota limitation the administrator may set. Once you have stored enough messages to fill your quota, the e-mail message may be returned to the sender.
For more information on the IMAP protocol, visit http://en.wikipedia.org/wiki/Internet_Message_Access_Protocol
POP
POP stands for the Post Office Protocol, and the primary differentiating feature when using POP connections is that it downloads the messages from the server to your device. This can be useful when importing messages from one account to another or for saving messages to your device, but for most modern uses IMAP is preferred.
For more information on the POP protocol, visit http://en.wikipedia.org/wiki/Post_Office_Protocol