Here's my quick take on the weapons, including the holes that I'm wondering about:
Anti-Matter Beam - this is the unknown
Blaster - 1/1/1 Range based PEN
Bore Missile - continuing damage
Burst Cannon - Increased PEN
Cluster Missile - seen in S:X
Cobalt Torpedo - 1/1/1 Extra Crew Hit
Disruptor - no clue
EMP Cannon - no clue
Energy Lance - inverted range modifiers
Fusion Torpedo seein in S:X
Gamma Ray Projector - no hull damage, crew hits?
Greek Firebomb  - no clue
Hyperspace Torpedo - Increased PEN
Ion Cannon - seen in S:X
Laser Cannon - seen in S:X
Meson Beam - no clue
Needle Beam - no clue
Neutron Torpedo - seen in S:X
Particle Beam - Halves Shields
Phaser - no clue
Phoenix Missile - may reroll to hit rolls
Plasma Bolter - DMG 2
Proton Missile - DMG 2
Pulse Laser - repeating
Resonance Cannon - Sheild rensonance
Rocket - Must reroll to-hit dice
Scattergun - doubled range modifiers
Stingray Missile - no range modifiers
Strike Missile - no range modifiers

-K

Thanks for the double check on those.  I'm still trying to figure out Needle Beams and Anti-Matter Beams.  I think for ballance purposes just choosing something that has a proportional WP modifier might work.

Dan,
do you still have this and could you post