POP
POP means that your email program will download the emails from the mailserver. The emails are not stored on the server if you don't select "Save email on server for X days"
Advantages with POP is that you don't take up space on the mailserver.
IMAP
IMAP means that your email program check new email but they are still stored on the mailserver. You can check your email from several units (webmail, mobilephone, computer etc) and they are not stored on them.
It is recommended to use IMAP if you use mobile phone or other mobile devices.