Code that does exactly what Vincent describes is here:
http://yelvington.com/annotate.php3
At one time I did some work on a file-based message board system, but ultimately found that it was not worth the time and energy to duplicate behavior that a database natively provides. If you want to create a reliable and scalable full-blown message board system with user registration and security, last-read-message tracking, user profiles, and so forth, it's much simpler to use MySQL than to constantly reinvent the wheel.