For all separately, as far as i know. That's what made the Metal Blaster from the Pitt in Fallout 3 damn powerful.
Well, technically what made it so powerful was not that each projectile checked separately, but that each pellet on a successful crit would gain a critical damage bonus that was disproportionate to the damage of that projectile. For example, the Terrible Shotgun did 80 damage per "shot" - roughly 8.9 damage per pellet with 9 pellets. However the critical damage bonus of this weapon is 40, and each pellet would gain that much of a bonus, meaning if a pellet crit it did 48.9 damage on its own. Combine that with a sneak attack (which does twice as much damage as a normal critical) which would guarantee that each projectile would critical, you wind up with some crazy total damage. I believe they balanced the critical damage bonus around VATS, which will only allow one critical strike to occur per usage of AP (per shot), so if you do crit with a multi-projectile shot only one of those projectiles could gain the crit damage bonus and the others would not. Unfortunately this does not apply to non-VATS shots leading to some rather broken damage scenarios.
This has been rebalanced for New Vegas (and rightly so), so that each pellet will gain a critical bonus proportionate to the base damage of the pellet itself. For example the Tri-beam Laser Rifle deals 66 damage per shot - 22 x 3 - but the critical damage bonus is 22 to match the damage of an individual beam.