IMAP creates a constant connection between mail clients (desktop and/or mobile) and Google Apps email.
Unlike POP, IMAP offers two-way communication between your web Google Apps email and your email client(s). This means when you log in to Gmail using a web browser, actions you perform on email clients and mobile devices (ex: putting mail in a 'work' folder) will instantly and automatically appear in Google Apps email (ex: it will already have a 'work' label on that email the next time you sign in).
IMAP also provides a better method to access your mail from multiple devices. If you check your email at work, on your mobile phone, and again at home, IMAP ensures that new mail is accessible from any device at any given time.
Finally, IMAP offers a more stable experience overall. Whereas POP is prone to losing messages or downloading the same messages multiple times, IMAP avoids this through two-way syncing capabilities between your mail clients and your Google Apps email.
If you're trying to decide between using POP and using IMAP with Google Apps email, we recommend IMAP.
http://mail.google.com/support/bin/answer.py?hl=en&answer=75725