Choose augmentations based on your play style, and get the ones that will benefit you the most.

Augmentation	How to unlock
Cranium	Capture is the most important, as you must be able to hack successfully. Do not waste points on Social Enhancer, Hacking Stealth, or Fortify.
Skin	Invest in the cloaking upgrade to keep your character invisible as long as possible.
Arms	Heavy Lifting will help open doors and move crates.
Torso	A faster recharge lets you use your special skills more often.
Eyes	Upgrade the radar and get the augmentation to see through walls if you have the points.
Legs	Being able to run silently is very useful, especially when you have enough energy to combine it with cloaking.