There are many alternate conversations that occur if you do something (finishing a mission/killing someone) before you're asked to:
If you finish the Statue of Liberty mission without visiting Harley Filben first, then go back to talk with him after you detain the head NSF terrorist, Filben asks why he stood around for an hour if no one wanted to talk to him, while JC tells him he found a back door into the statue. Filben then insists that he wants extra pay, and JC tells him to take it up with Manderley.
Sgt. Kaplan (the soldier patrolling the front gate of UNATCO in the first mission) has different dialogue if you wait to talk to him until after the NSF commander is apprehended.
If you choose to handle the situation in the Battery Park subway station before clearing out Castle Clinton, Anna will have extra dialogue praising JC's abilities.
You can get a special conversation with Filben later on if you kill tabloid reporter/UNATCO spy Joe Greene before you're asked to. Likewise, Manderley chews you out for executing a civilian if you kill him during his first appearance at the Underworld Bar.
Filben will also have special dialog if you first talk with him during the third Hell's Kitchen visit, having skipped his previous appearances.
If you decide to glitch through the NYC sewer grate during the MJ12 mission for Smuggler without going to see him first, when you get to the end, JC will ask Ford Schick about the identity of the soldiers, and not have any clue about Smuggler's task.
When you go perform the NSF transmitter mission for Paul in Hell's Kitchen, it's possible to kill all the friendly UNATCO troops in your way. Doing so will net you different dialogue after you activate the transmitter from Walton Simons, who says he always knew you were a traitor like your brother. If you do only non-lethal takedowns before you activate the transmitter, he will congratulate you for your forethought.
If you kill the NSF commander (via discovering his secret room) in the abandoned subway tunnels before doing anything else, JC has additional dialogue with a young boy if you haven't talked to him yet. The boy tells JC the secret of how to access the room, and JC then tells him not to go near it because it's "not too pretty in there".
The dialogue with Walton Simons changes during the UNATCO escape if you kill Manderley before triggering his conversation (which is usually done by tossing a LAM or firing a rocket into the room before you enter). Simons brushes the death off and says Manderley was expendable, before commenting that it has no bearing on his plans.
If you obtain the proof of Maggie Chow's guilt in the police station before visiting Gordon Quick (which shouldn't be possible because the player doesn't know the code to the station/vault unless they speak to her), JC will tell Quick that he already investigated the station and found what he needs, and Quick praises JC for having the guts to go through with such an act. The rest of the conversation takes a decidedly different tone as Quick tells JC to find the sword and stop Chow.
If you kill Jordan Shea, the augmented bartender, before the superfreighter level, Vinny will chuckle, "Someone offed the bartender - drinks are free!"
If you kill the cemetery groundskeeper before you talk to Stanton Dowd, he will comment on how Properly Paranoid you've become.
If you take too long exploring the mansion in France, or poke around in unimportant areas, ICARUS will contact you and ask, "What are you looking for?"
During the final boss fight (which isn't really a "fight" so much as trying to survive the whole room trying to kill you), you can enter some ducts here and there. Coming out of a duct the same way you went in has Bob Page mock you. "Lost?"
In the end of the tutorial level, it is possible to reach the observation window by stacking some boxes and climbing them. If you do it, you actually get complimented for it.
The game will acknowledge the use of glitches. Throw a Gas Grenade at UNATCO's front door during the first level, then run past the guard that comes out. Once inside, a guard will actually acknowledge you skipped a bunch of terrorists that way. The game continues normally as if you just finished the first level legitimately, but not before acknowledging your ingenuity.
If you manage to shoot the seagulls that are flying just off the Liberty Island pier in the opening mission, Corporal Collins admonishes you with special dialogue ("I don't understand! What are you doing?").
In the Statue of Liberty, after detaining the head terrorist, you can shoot or knock out the UNATCO soldier that's coming up. When reporting for debriefing, your boss asks you if you know what happened up there.
When you visit UNATCO later in the game (during Walton Simons' visit), you can watch the interrogation of the terrorists captured in Castle Clinton. You can go into the cell once the doors are open, watch the interrogation, and even execute or interrogate them by yourself. The interrogator (Walton Simons) is not amused, and tells you so, as do his goons. Conversely, leave him alone, and said goons will thank you for being considerate of their boss.
If you decide to kill all the Rooks except for El Rey in the abandoned subway station, leave him to run around until he becomes passive again and then talk to him, there is an alternate conversation where El Rey urges JC to be cool. JC subsequently threatens him and either tells him to go back to school (while receiving the LAM), or tells him he wants more (causing El Rey to throw the LAM at you and start running). If your inventory is full when you ask for the LAM, JC has a unique response where he chuckles and tells El Rey to wait a moment.
If you knock out, but not kill, the drug dealer El Ray asks you to remove El Ray will complain about you not killing him with JC commenting that he used the 'the minimum required force'. Ultimately El Ray says he will send someone to finish the drug dealer off before providing you with the LAM.
During the Airfield level, when you discover that Paul is working for the NSF, he asks you not to shoot any of the (now identified as friendly) unarmed NPC's standing around the plane. If you do, he chews you out for it.
When you are about to arrest Lebedev, Anna storms in and orders you to kill him. If you decide to kill her instead of Lebedev, you get an entirely new cutscene, where Lebedev informs JC that his parents were lab technicians, Alex will delete the audio transcripts of the prior few minutes and JC ends up lying to Gunther to cover his whereabouts during the shooting. The fact that nothing in the game clues you in to this makes it all the more shocking when it actually works. Killing Anna also impacts the rest of the game: when you're captured by the conveniently invincible Gunther Hermann, he gives you a special message about making you pay for her death after you escape confinement. Also, Navarre stays dead for the rest of the game, meaning the boss battle is skipped.
Alex will also give you a What the Hell, Hero?, both on the infolink and when you return to him at HQ. JC will growl, "Agent Navarre was out of line."
This also has another variation. Plant a LAM outside of the room you meet Lebedev, then listen in the background as she's blown to bits not long after Lebedev surrenders. By skipping the dialogue with Anna before she tries to kill you for not offing Lebedev, the same events happen, but Gunther will instead cotton on that you killed her later, as you are escaping UNATCO HQ.
If the player goes to the Underworld Tavern or Smuggler's after escaping the raid on the 'Ton Hotel (despite having no reason to do so), the characters will have extra dialogue reacting to the raid and telling JC to get out of Hell's Kitchen immediately.
If you kill Louis Pan when you get to Hong Kong, Gordon Quick will admonish you for the act using special dialogue. Evidently, the programmers expected that gamers would be so fed up with Pan's annoying statements that they would shoot him. Alternately, if you knock out Pan instead of killing him, Quick will say the same dialogue except for the line, "He was a good earner," which becomes, "He is a good earner."
If you somehow manage to get on the train near Castle Clinton without first resolving the hostage situation one way or the other (a feat that is supremely unlikely given that the hostages, the laser triggers for the explosives they're trapped with and all the terrorists are between you and the train), Paul will admonish you with special dialogue when you arrive in Hell's Kitchen.
If you barge into the women's bathroom, your boss chastises you for it later. (Mass Effect 2 has since done so as well.) The woman you encounter, Shannon, will also behave differently toward you for the rest of the game. If you don't go in, then she generally acts civil and friendly. But if you do into the bathroom, she'll never let you hear the end of it. In your next meeting with Manderley he will reprimand JC on his intrusion into the women's bathroom as "unprofessional".
Shannon will later admit to you that she's the one who's been stealing weapons and ammo from the armory if you go and see her in the break room of UNATCO HQ while you're breaking out of there after being captured by Agent Hermann or Agent Navarre. She'll also offer to sell you scrambler grenades. If you then go back to Sam Carter (or talk to Shannon before seeing him) and talk to him, JC will inform him who the armory thief was, and Carter will then reveal there's more to the story than you know, and Shannon's gonna be facing an ugly surprise in the morning.
There are a whole range of options that result from the character of Sandra Renton. Not only can she live or die based on whether JC rescues her from Johnny or not, but how he deals with Johnny influences later actions. The later conversation with Jojo at the 'Ton can also result in several scenarios: give Gilbert Renton a gun and stay at the hotel with her father, knock out or kill Jojo yourself and Sandra will leave in disgust (before appearing later in the game at the abandoned gas station), or give Gilbert a non-lethal alternative like a crossbow to defend himself. It is also possible to meet with Jojo before the confrontation and kill Gilbert and Sandra on his behalf instead.
If Sandra Renton dies prior to JC visiting NYC for the third time (usually as a result of player action), when asked by the soldier in the Underworld Bar if he knows her, JC will lie and say that she was killed by Jojo Fine.
Similar to the System Shock example mentioned on the main page, getting a basketball through (or very close to through- off the backboard and rim works as well) a hoop in Hell's Kitchen will spawn the message, "Someone sign him up for the Knicks!"
If you do this the first time you're in Hell's Kitchen and then do it again when you return, you'll get a different message - "You should be playing football - Go Cowboys!" (Ion Storm was based in Texas.) On your third visit to Hell's Kitchen there is yet another new message for doing this.
There's a sick man in Battery Park who begs you to kill him. If you try, he doesn't turn hostile and flee like most NP Cs. (The police don't seem to care either, though that's less the dev team thinking of everything and more the dev team crafting a convincing dystopia.)
Deus Ex: Invisible War
The mission at Mako Ballistics to either find, analyze and register the prototype of a Rail Gun for the WTO or kill the lead scientist for the Order. This is usually mutually exclusive because opening the canopy for the weapon closes the door to the scientist and killing him first will disable the switch to open the canopy in the first place. You can however trick the door by placing one of the boxes on the floor underneath the door, forcing it to stay open when it would normally close. Analyze the gun (netting you a "mission accomplished" from the WTO and a bonus later on), then go to the scientist. You'll need a ammo-free weapon like a knife or blade to kill him because his health is abnormally high at this point. When finally killing him, you'll receive a "mission accomplished but it was too late" instead of a normal "mission accomplished" from the Order and later on you are chewed for still helping the WTO. Bonus points for that regardless, you get the Order's bonus later on as well.
Later on, you get the option of killing the security chief in the Arcology, or letting him live so he'll give you the code to activate the nanobots for the plague cure. It's entirely possible to do both, as depending on which missions you did beforehand, the chief will still be in his office even after you activate the bots, so you can cure the plague, go kill him afterwards and get your reward from the harvester.
NPC's will keep track of your actions, if you kill schoolgirls at Tarsus Academy, Donna Morgan will chew you out over it. You can kill most NPCs, which will automatically complete their missions. You can get rewards from other characters that aren't listed as missions-If you talk to Dr. Nassif after you find his daughter, he'll give you 200 credits(and if you killed Silas, Alex will mention that and Nassif will ask you if you're sure Silas was behind the disappearances); and after you bribe the manager of NG Resonance to endorse Peequods or Queequegs, you can tell NG about her manager taking bribes and you'll get 200 credits for it.
There's also a hidden ending which you can get by flushing the UN flag in the toilet, which opens up a dance room with all the characters and comments from developers are seen floating around the room.
Deus Ex: Human Revolution
The first dialog "boss" of the game, Zeke Sanders, can be handled in a multitude of ways, and practically every single one has an outcome. Kill him, or let him try to escape with the hostage? His corpse will be in the morgue. Fight him, and knock him out? He'll be in the cells in the police station, and be about as pleasant as you'd expect. Let him go? He'll contact you later with a pocket secretary containing information on the secret FEMA base you invade. If during the latter you decide to not kill him, he'll appear later as an enemy when you're going after his brother in the sewers, or you can just kill him then and there.
For several months after the game's release, it was thought that the Social Enhancer (CASIE) augmentation didn't work on/display any information on Sanders, given that it was the first real mission of the game and no one could gain enough Praxis Points to unlock the augmentation. However, it turns out that if you travel through every duct, hack every system and (non-lethally) take out every enemy (a feat which is supremely unlikely), you can get the two points required to unlock the enhancer, which will display psychological information on Sanders. However, it doesn't allow the player to use the CASIE to talk or influence Sanders into surrendering.
If you go into the women's bathroom on your quest to do everything you can, Pritchard will slip a casual disapproval into his dialogue when you meet with him.
If you wait too long at Sarif Industries before going to the first mission, assuming that it's a video game and the mission won't start until you start it, the hostages will be dead before you even get there. Even better is that several characters will chew you out after the mission for waiting.
On the "Lesser Evils" sidequest on your first visit to Detroit, Brian Tindall asks you to knock out or kill a pair of drug dealers that are after him for giving away neuropozyne. However, if you already took them out beforehand, accepting the mission will give a unique dialogue where Jensen will say so right after Tindall mentioning their names, which in turn gets a veiled insult about Adam being overly violent.
Likewise shutting down the jamming frequency in Derelict Row before you're even asked to warrants a unique response from Pritchard, and connecting the neural hub at your apartment immediately leads to Malik being sent to take you to Highland Park (however, there is no explanation why she needs to pick you up at Derelict Row). Especially odd, considering your apartment building has a helipad on the roof. But they even thought of THAT, as the elevator to the pad is stated to be out of order.
Isaias Sandoval will generally be trying to kill himself if you planted the evidence of his involvement with the Tyrants or mention it while talking to Taggart, but through some luck and use of CASIE it's actually possible to get Taggart to tell you where he is without publicly revealing Sandoval's secret. Of course, this being Deus Ex, you can completely bypass Taggart and either sneak or blast your way into Taggart's room to get the information yourself. If you follow either of these paths, the social battle where you talk Sandoval out of killing himself doesn't take place and he will try to kill Adam instead.
The final boss is behind a bulletproof glass shield. You can go through the long and complicated process to open it up, or you can just use the wall-penetrating laser rifle to kill her immediately.
If someone has something valuable on them, you can just punch them in the face to take it. Among these punchables are Anonymous X and Brian Tindall, both of whom possess quest-related items. In the case of Anonymous X and Chuanglia, if you agreed to pay them (which you need to do for the latter), then when you knock either out they'll have the money on them. However, if you take a quest to pay some thugs protection money to make them get off a girl's back and then knock out the thug and take the money back, the quest will be failed, as they have no reason to leave her alone now.
What's more, if you do it while invisible so no one sees you, they won't know it was you, and you can walk out of the bar (after becoming visible again) and no one will harass you. The quest will also be successful.
If you steal things from other people's offices in the Sarif Industries HQ, you'll eventually get several emails asking you to investigate the mysterious "office bandit". These emails will give you several door codes, making it easier to clean the rest of the building out.
If you sneak into The Hive before visiting Hengsha Court Gardens when you first arrive in China (something you wouldn't normally think to do), an alternate cutscene plays where Tong talks to a Belltower operative about Van Bruggen.
If you do this instead of speaking to Tong the next time you see him he won't mention that the two of your are supposed to be friends.
In The Missing Link, if you knock out all of the soldiers (instead of killing them) on the way to meet the person who set you free, Keitner will say different dialogue, and mention that you put a lot of her men into comas (instead of killing them).