POP stands for Post Office Protocol, which basically means mail is delivered to your mailbox on the server and then your computer logs on to the server, collects the mail and puts them in your mail program. This way each time you collect your mail, they are removed from the server and placed on your computer.
IMAP stands for Internet Message Access Protocol, this is where all of your emails are stored on the server and your mail program accesses the email and displays them in your mail program. With IMAP, you manually need to purge or delete the emails from the server as with IMAP they won't be removed from the server when you access your email.