I have a Shaw mail account (Shaw is an internet, cable and home phone provider here in Vancouver Canada) and they allow email access through a POP service... so I have set up my iPhone mail to access my Shaw mail as a POP account. It works great, but to answer the original syncing question, with this type of account and set-up... no my mac and iPhone do not sync actual messages... only account settings. Which is kinda stupid if you ask me, once my account was set-up I turned off mail syncing in iTunes because it does nothing but sync settings which once you've set them up, don't ever change.
So, if I receive and email on my iPhone, read it, reply to it and delete it, then sync to my mac, that email still shows up as unread in my inbox on my mac and no deleted or sent messages from my phone end up in my sent or deleted folders on my mac. Hope that helps. But again, after saying that... I think it is still awesome to have the ability to receive, read, and reply to my personal emails on the go and am willing to forgive the non-syncing for the great access and the other amazing features of the iPhone. Hopefully in a future update they'll add syncing for POP accounts.