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POP3 and IMAP are two different protocols for retrieving and managing your email.
Advantages: POP3 is good to use if you don't have an "always on" internet connection, because after retrieving your email you can disconnect your internet connection and read your email while offline. It also takes up less server-side storage space since your email only stays on the server until you download it.
Disadvantages: The main disadvantage to POP3 is that, for example, you had a computer crash and lost all your email, there'd be no way to retrieve it since it would only be kept on your computer. Also, if you are away from your computer that you've downloaded the mail on, you have no way to access those email messages remotely. It is also slow, since "checking mail" involves downloading every email in its entirety to your computer.
Advantages: Storing your email on the mailserver means you can access your email from anywhere! If you are travelling, in the computer lab at school, or at work, you could use any IMAP-enabled email program (Outlook Express, Eudora, Netscape, or our Web Mail program, among others) to quickly access all of your current and saved email. Since all your email is on the server, your email is safe in the event that you have a computer failure or corrupted email program.
Disadvantages: you need to be connected to the internet while accessing your email. If you have a great deal of email, using IMAP can take up lot of your email account storage space.
zNET's mail servers support both POP3 and IMAP access, and most email programs support both protocols nowadays, so you can choose to use whichever you prefer.