As with so many other things, the start of the answer is, "It depends on the circumstances..."
If you're supporting users who retrieve email from multiple machines, then IMAP is the way to go, since only copies of headers are loaded to the clientuntil the message is actually opened. The downside to this is that the server gets loaded up with messages (many users NEVER delete messages) unless a 'retirement' policy is set up that email messages are deleted after X days (pick your X)
POP3 is the most common, since it was the first (I think). It doesn't really have all the features that some users would like, though; for instance, it doesn't give you the option of previewing the size of messages before downloading them, which can be a real annoyance on a slow modem line.
Good Luck!