[spoiler]10mm pistol, Revolver and Sniper Rifle. The first two tricked out as far as I can get them. Sniper Rifle with Laser Sights because damn that upgrade is overpowered. It lets you basically use it scopeless however and whenever you want. Silenced 10mm allows for silent headshot kills (especially with armor piercing upgrade) and high ranges and Explosive Revolver lets you take down almost anything else with ease during combat. It'll tear apart robots and in the third (and hardest) bossfight it's ridiculously overpowered as it just shreds the boss.
Augs, well... I had most of them, I think. Hacking very high, as that is useful from the get-go and all the way through the game. Punching through walls. Dual takedowns (even if that is situational and I rarely used it). Electricity/EMP immunity as that makes two bossfights (second and last respectively) completely trivial. Invisibility for slipping through laser grids/past cameras in some cases. Seeing through walls aug, but I very rarely used it. Rebreather for gas/poison immunity was useful in a couple of places.
Oh, and maxed inventory space augs and power cells and regeneration of those.
Can't recall what else I had.[/spoiler]