Well one way is to use a servo to fire the trigger. That doesn't rely on knowing any details about the protocol used to fire the projectiles. Here is a video on how to use a servo to fire a camera shutter that madmeco sent me today: Remote controlled finger. Give any camera remote shutter capability, and laser. - YouTube
Then there is instructable on how to fire a Nerf Vulcan via arduino: http://www.instructables.com/id/Arduino-Controled-Nerf-Vulcan/
If you can figure out the protocol, there is this USB rocket launcher: http://www.thinkgeek.com/product/8a0f/