The Dev Team Thinks of Everything/Deus Ex

The Deus Ex series is chock full of this.

Deus Ex

 * 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.
 * You can get a special conversation with Filben later on if you kill before you're asked to.
 * 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 transmitter mission for Paul in Hell's Kitchen, it's possible to kill all the  in your way. Doing so will net you different dialogue after you activate the transmitter from, 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.
 * 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 kill Jordan Shea, the augmented bartender, before the superfreighter level, Vinny will chuckle, "Someone offed the bartender - drinks are free!"
 * If you kill the 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.
 * In the Statue of Liberty,, you can shoot 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 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.
 * During the Airfield level, when you discover that, 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, storms in and orders you to kill him. If you decide to , you get an entirely new cutscene, where . The fact that nothing in the game clues you in to this makes it all the more shocking when it actually works. Killing  also impacts the rest of the game: when you're captured by the conveniently invincible Gunther Hermann, he gives you a special message  after you escape confinement. Also,  stays dead for the rest of the game, meaning the boss battle is skipped.
 * 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 Anna later, as you are escaping UNATCO HQ.
 * 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.
 * 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 chastise you for it later. (Mass Effect 2 has since done so as well.)
 * The woman in the bathroom (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 . 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.
 * 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!"

Deus Ex: Invisible War

 * The mission at Mako Ballistics to either find, analyse and register the protoype 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. Analyse the gun (netting you a "mission accomplihed" 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 hecause 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 accomplsihed" 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 dissapearances); 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? Fight him, and knock him out?  Let him go?  If during the latter you decide to , or you can just.
 * 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 as soon as soon as Tindall mentions their names which in term gets a veiled insult about Adam being overly violent.
 * Likewise shutting down the jamming frequency in District 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.
 * Isaias Sandoval will generally be trying to kill himself if you planted the evidence of 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.
 * The final boss
 * 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 Anonymous X's case, if you agreed to pay him his "handler's fee" and get the evidence, then when you knock him out, he'll have the money you paid on him instead.
 * Ditto for another hapless informant. 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.