All right, I just finished the game as a Pacifist Jensen on Give Me Deus Ex difficulty. I had a very easy time with every single boss.
So some tips:
-Grenades are important. Make sure you come into each boss battle with a few Gas and EMP grenades, which will stun the bosses (except for the third one. He seems to only be stunned by Gas grenades).
-Stun Guns: With the second boss, I kept her stunned the entire time. Seriously, she ran at me and I went all *Brzzztt* and she stood there for a minute while I alternated lobbing grenades at her and re-stunning her. Ridiculously easy. This didn't work on #3, though (and I didn't try it with the first guy).
-Rocket Launchers: I know I found a Rocket Launcher not long before the first boss, and I found a few more elsewhere as well in the game. It was really my go-to weapon for the first one, though. I'm not sure how good it would be against the other bosses anyway. The Rocket Launcher is slow to equip, slow to fire, and makes it slow to throw grenades (and since bosses #2 and #3 are both rather mobile so long as you don't have them stunned, being slow is a bad thing). Use it on the first guy and maybe keep it as insurance otherwise if you wish.
-Keep a weapon throughout the entire game. For me, I kept the 10mm pistol since it was small and I didn't want something bigger taking up space the entire game (lethal weapons were useless to me outside of boss fights since I took the pacifist route). The advantage here is that you can keep upgrading the same weapon over and over.
-Typhoon: I only used this twice in my entire playthrough, and both times on the third boss. But it killed him very quickly (I stunned him with a gas grenade, used Typhoon. Stunned again, Typhooned again. Then he died).
-As far as augmentations go, the only ones I found useful against bosses were the Typhoon, the cloak (and energy upgrades. They go hand-in-hand), and chemical resistance (kept me from being affected by my own gas grenades).
