In Mail.app I have an IMAP uni email account and a POP email account. There are pros and cons to both.
IMAP is great, as it gives you very speedy full control over your mail box on the web. However, you have to be connected to the internet to read most of your mail, as only a little is cached (think this can be adjusted). The best thing of IMAP is that changes are made on the server, so if i do something on one computer it'll be reflected on every computer. Mail clients are obviously easier to use than many webmail clients so being able to use any mail client (entourage/outlook/mail/etc) and see all my mail up to date with changes etc is a big bonus.
POP is good cos you save the emails on your computer and the text is faster to search, but deleting mail doesn't delete them on your server, which is extra work (unless you've set them to delete after they've been downloaded).
I'd never used IMAP until university and I have to say I like it a lot. It's fast, easy and gives me full control of my uni space.