Firstly, a disclaimer. I have not finished the game as a pacifist due to reinstalling windows and not backing up the save games. However, I did get to the Paris catacombes on 'realistic'. I believe I was on around fivety saved games at that point, so it is possible without quicksaving your way through. This was not even playing particularly optimally, since I was trying out all the augmentations I didn't use on my initial playing.
Secondly, another disclaimer. This is an action game, so I'm not that pacifist. My loose definition of pacifism means that I'm allowed to knock people or creatures unconcious, I'm allowed to destroy machines like the patrolling robots, I'm allowed to 'accidentally' cause situations where other people kill people for me and that I'm allowed to kill plot objects where my killing them is a requirement for getting further.
With that, on with the tips:
Weapon Selection - the pacifist ones
You're a pacifist, right. So when fighting people, that cuts you down to a pretty limited selection consisting of the police baton, riot prod, crossbow with the tranquiliser darts, pepper spray, and gas granades.
The pepper spray is probably the worst of these, because you have to get pretty close to someone to use it, it doesn't have a large area of effect and it doesn't knock people out very effectively. You may as well carry it along (you'll have lots of inventory space due to the lack of bulky weapons) but its use will be pretty limited.
The crossbow is not particularly useful either, because between the person being hit and going down, they have enough time to raise the alarm. In specific circumstances, against animals, or where you can wait for the alarm to die down and people to return to their peaceful state, this is good. In most, it isn't, especially since the supply of tranquiliser darts is limited.
The riot prod is an excellent weapon - if you can get close to someone you can quickly take them down. It has the drawback that its ammo supply is very limited.
Gas grenades are nice area effect weapons - useful for taking out clumps of guards, or at least keeping them off your tail.
However, your best weapon remains the humble police baton. Certainly, it's not effective to start with, but with a little patience, you can go far...
Skills Selection for weapons
The first thing you want to do is decrease your skill with the pistol to zero - you won't need it much. Get one level of computer hacking (you can get around a lot of problems by hacking into the computers, and you can only do this with some skill in it) and dump the rest into melle. Once you've got to advanced, you might want to increase lockpicking and electronics before becoming a master, but that's your call.
Augmentations for weapons
The second part of the combo making the police baton useful is the combat strength augmentation - collect that and upgrade it every chance you get. Once you've got reasonable levels of combat strength augmentation and melle skill, then you can use the baton like the riot prod - go up to them, whack them, they're unconcious.
Weapon Selection - other ones
You will also wish to take:
A pistol, for setting off LAMs, exploding barrels, etc.
A Dragon Tooth Sword, for hitting things hard with (with high melle skills and combat strength you can knock things with strength up to about 75% down with this thing - usually you need LAMs for something like that)
A GEP Launcher, LAMs, Scramble Grenades, EMP grenades, for taking down annoying robots, turrets, buildings, etc.
Run Fast - this augmentation is absolutely essential. Upgrade it to the maximum. The number of times you can just run past problems is amazing. An army of three hundred troopers converging on your position? No problem. Just turn on run fast, sprint to the exit of the level, and slam on a medikit for the couple of bullets that grazed you. And, more importantly, it allows you to run past the boring bits quickly, and thus get onto the fun bits of interaction.
Self Healing - another essential. No longer do you need to worry where you're going to find your next medikit / chocolate bar / soda. You just turn on self healing, and your problems melt away. Now you only have to worry about maintaining your Bio-electric supply. When highly upgraded, it gets even better - you get to the point where you can't drown, be set on fire, poisoned, etc. effectively because you can just heal any damage you take that way away before it gets problematic.
Fire Control - this one is quite useful as it gives a boost to targetting - and since you won't have spent many skill points on that, a bonus is always useful. Secondly, the additional info screen allows you to reduce a target's health in a controlled way, so that you only need one tranq. dart to knock them unconcious, whereas otherwise you could waste several.
Energy Efficiency - Reduces the Bio-Energy you use when running and healing. 'nuf said.
The rest are pretty much of a muchness, and so choose which you feel like taking.