If all you want is to have the same INcoming mail on both machines, that's simple. Just set each machine's mail clients Account settings to leave mail on server for 10 days (or Delete mail from Server after 10 days, depending which mail program you use). Then just make sure you check mail on each machine not less than once every 10 days.
If you want to synchronize your Sent items, that's more difficult, unless you just BCC every sent mail to yourself and have a rule that puts mail from yourself into a Sent folder automatically.
If you want to actually sync all of your mail folders, then I don't know how to do that with a POP3 account.
What I do is sync my laptop and desktop (normally once or twice a week) using SuperDuper. So essentially my laptop is an exact clone of my desktop, mail and all. It works well for me and ensures that I have a complete backup in case of any failure.
-The first clone will take a couple of hours. After that the "smart update" function makes it a lot quicker.
-Difference in HD space between the two machines. If your laptop (I'm guessing that machine will have the smaller HD) has 40GB of HD space then your clone image can't exceed that. Not an issue for me but might be for some.