Really depends what metagame you like to play.
If you've been getting top tier weapons all game like Burst Laser II's, I would suggest offensive augments like Pre-Igniter and Auto-Reloader.
If you've been getting tons of drones, I would suggest Defense Scrambler.
If you get lots of boarders (like me), nothing beats Zoltan Shield Bypass, O2 Respirators, and Reconstructive Teleport. So your crew won't die porting back due to a stray missle.
If you get lots of Shield Drones, and a Zoltan shield, I would suggest stacking Shield Charge Boosters for that super tankiness during the final fight.
Of course, now I will rate on what I think is best to worst.
#1:
Zoltan Shield: Best Augment in the game, hands down. Reliably protects your from missiles, teleports, hacks, and mind controls. Hacking just delays the super-weapons, engines only gives you 55% chance to have the thing miss, and cloak has a huge cooldown. Zoltan Shield is the only reliable augment that does all these things. Only if it doesn't go down.
#2:
Automated Re-loader/Shield Charge Booster/Pre-Igniter: These things will help your tankiness/firepower. As the Romans said, the best defense is a great offense. Both 'defense' and 'offense' are interchangeable.
#3:
Boarding Augments: Not as useful as everything above, but if done right can lead to some serious micromanagement outplays. Like what I do on a daily basis. Mantis B OP.
#4:
Scrap Recovery Arm: Early game this thing is a godsend. Everyone can tell why. Late game this thing is just a thing that takes up a slot.
#5:
Fire Suppression: "Oh shit, my doors/oxygen are on fire, and my crew is low! What am I to do? Oh wait, what fire?"
Just a serious playmaking tool.
Honorable Mentions:
Reverse Ion Field: Difference between Life and Death vs engies, those guys have like 30 ion weapons each.
Hacking Stun: You can outplay a room full of Mantids if you play it right.
Rock Plating: Doesn't negate damage as reliably, but still might save you if your ship is on like 2 hull and you keep resisting damage.
Distraction Buoys: Might save your butt from being pulverized by a elite fighter. MIGHT. (refer to Nesasio run #3
)
Long Range Scanners: Knowledge is (almost) power.
Trash:
FTL augments
Repair Arm (droney is better. And I hate the drone. The drone is nothing to me but a situational playmaking tool/47 free scrap)