I use both phenolic, and fiberglass boards. I drill them with a drill press and use either 4-40 or 6-32 threaded spacers, most are about 1/2" long. Sometimes I use M/F threaded spacers.
For cleaner holes you could also put a piece of thin board over the top and bottom and clamp that as well, it prevents the 'blowout' mess that a drill tends to leave when it punches through and will help against chipping when you start the hole, the denser the board you use the better.