Lead Target Assistant (1500 cr.)
I consider this one of three indispensable cards. It calculates where you should fire your primary weapon so that it will hit your opponent, assuming it stays heading in the same direction and at the same speed.

Combat Scanner (3250 cr.)
The second of my three. Tells you how much shield and hull strength is left, so you know what weapon you should use.

Afterburner (2500 cr.)
The last essential. Just in case you've been living in a cave until now, afterburners let you crank your speed for a limited time. It uses up your Afterburner reserves when in use. (they do recharge) Use the TAB key to activate it.

Radiation Screen (4850 cr.)
Limited use: prevents you from taking radiation damage in the Cassitor's Station and Twilight Field sectors in the Twilight region.

Aim-Point Module (3800 cr.)
Adjusts you lasers minutely so that when you fire, the lasers are aligned along the centerline of your ship at the exact distance of your target.

Advanced Radar (3250 cr.)
Cuts through jamming. Also prevents radar "jumping" in storms.

Fog Radar (3250 cr.)
For use in the Twilight region and Hephaestus sector. Cuts through the Fog.

Lateral Thrust (6250 cr.)
Allows you to strafe using the S and D keys. I don't know where this becomes available, I've never actually seen it in single-player (without using a cheat code.)

Boosters (3800 cr.)
Boosts your ship's top speed (and Afterburner top speed) by 25%.

EW Jamming (6500 cr.)
Helps prevent radar and missile lock-on.

Lock-on Defense (5650 cr.)
Drops a bundle of energy to try to confuse missiles. Hit C to use it. You only get 30 usages per mission.

Lock-on Warning (3650 cr.)
According to the Read Me file, the in-game description is wrong and this upgrade tells you when someone targets your ship.

Smart Shields (4650 cr.)
Automatically balances power between front and aft shields. Also decides what percentage of energy should be diverted to the shields from the engines. I'd like it better if all it did was balance the shields and allowed me to decide about the energy.

Tracking Enhancements (3750 cr.)
Decreases missile lock-on time by 25%.

Burn-Off Device (4500 cr.)
Tries to fry sappers by firing an EMP stream at them. It's automatic.

Laser Reserves (3500 cr.)
Increases your laser energy by 25%.

Shield Reserves (2300 cr.)
Increases your shield energy by 25%.

Afterburner Reserve (2800 cr.)
Increases afterburner energy by 25%. Note: There is absolutely NO reason not to take this upgrade: it has a reserved slot (no pun intended... for once) that nothing else can use.

Ammo Hold (1200 cr.)
Wanna guess? Yep, you're right. Increases the number of missiles, rockets etc. you can carry by 25%.