I personally think that a really good message board should be backed up by a fast database like MySQL, and PHP has some of the easiest interface functions with MySQL and mSQL out there. I'm fairly certain that JP uses a MySQL backend for these forums. Almost any CGI script can be written to be just as effective as a PHP/MySQL solution, but I think for ease of coding, PHP is the best choice. I've done a lot of work with MySQL databases and PHP has proven to be the best interface to MySQL I've found.

There's an excellent book out there called PHP and MySQL Web Development that goes over the fundamentals of PHP, then the fundamentals of MySQL databases, and finally some real world applications of both (such as a content management system, a mailing list manager, and a web forum. I've used it extensively, and the info is pure gold. Here's the info:

PHP and MySQL Web Development
by Luke Welling and Laura Thompson
ISBN: 0-672-31784-2