Gimme the GEP gun.
I mean...
Give JC the GEP gun.
Anyways, I'd suggest taking the leg augment that speeds you up rather than the one that lets you run silently, since crouching and moving renders you silent anyway.
Just crouch, activate speed boost, and zip around super stealthy like.
Oh, and if an NPC asks for a gun, drop the one you're using and find them some generic one to use, since you'll be modding your guns and won't want to lose them.
And Men in Black/Women in Black explode when you kill them. Knock them out with a baton sneak attack or cattle prod and they won't. Plus you can loot them.
Search every nook and cranny for secrets and loot. Hack everything for door codes and what not. Explore the vents.
Stealth pistol is pretty handy.
Blind people with your flashlight eyes.
Tranquilizer darts are a bit... odd. You'll see what I mean.
Drink lots of booze.
Watch out for A BOMB!