Consync has an article up comparing the two most popular protocols for accessing your email on a Pocket PC, Smartphone, or other mobile device – POP3 and IMAP:
Email is email, right? Not exactly, there are a pair of standard protocols for email and each has it’s own place in this world. POP3 (Post Office Protocol 3) and IMAP4 (Internet Message Access Protocol 4) can be accessed from a Windows Mobile PocketPC or SmartPhone. They each have advantages and disadvantages and in this article we will look at each type of email protocol and see what is best for what you need for your mobile communications.
Go read the article for the nitty-gritty details. It’s a nice overview of the features of POP3 and IMAP, if you’re not already familiar with them.
Personally, I’ll always use IMAP for accessing my email on my Smartphone and Pocket PC, because IMAP better supports storing the mail on the server and accessing it from different devices. I use Hotmail for my personal email, and in a typical day, I’ll access it in various ways. First thing in the morning, I’ll check my mail on my Smartphone on my bedstand, which is configured to access my Hotmail account via IzyMail.com (for $10/year, they’ll act as an IMAP gateway to web mail accounts like Hotmail). Later in the day, I’ll keep up on reading and sending mail using the Hotmail web interface or Outlook on my computer. In the evening, at home, if I’ve got a couple of emails to write, and don’t want to use the keypad on my Smartphone, I’ll pull out my iPAQ 4350, and read and send using the Inbox application over WiFi (again, through IzyMail). The reason I love IMAP is that it lets me access the same mail account from 4 different devices/methods (Smartphone, Pocket PC, web, and Outlook) and it keeps all of my messages in sync. Mail that I’ve read and/or deleted on one devices shows up as such when I check from another device. All in all, it works very well for me.