Mass Effect does this a lot. Given that there are a high number of variables that carry over through the series, it often leads to unique dialogue choices and gameplay options, even in situations where they wouldn't seem apparent.
Mass Effect 1
Most players choose to pick up Liara early on, as she's a valuable teammate. However, if you delay until you have completed the other available main story missions, she reacts accordingly. She starts off certain that she's hallucinating your arrival and, during the post-mission briefing, is understandably bamboozled by all the information you're throwing around. She's even offended that you've figured out in a few weeks something she hasn't in decades of study.
When visiting the Peak 15 Rift Station, you will encounter Captain Ventralis, and at the end of the conversation a pair of rachni soldiers will attack. You can fight with Ventralis and kill them, or simply bolt up the hallway behind him and let him and his lackeys deal with it. If you do that and return, Ventralis will have some select words for you. Almost no one is going to leave Ventralis to fight alone in the first place, as most fans don't even know the option is there to run from that encounter.
Upon entering the Artemis Tau Cluster, you get a message to meet Nassana Dantius at the Citadel. However, if you put that off and instead chose to explore first, you end up discovering a slave ring on Sharjila run by her sister. When you do eventually show up to meet Nassana on the Citadel, she will ask you to "rescue" her sister from a group of "mercenaries". Shepard angrily reveals that they know the truth about her sister, leading Nassana smugly to reply that she doesn't care, admitting she was planning on having you kill her sister anyway.
On Virmire, Wrex can possibly be killed if you cannot convince him to help you destroy Saren's genophage cure. However, if you haven't recruited Garrus and Liara, he'll back down even if you don't meet the persuasion requirements and didn't do his quest.
If you get enough mission requests from Admiral Hackett in a very short period of time (about three or more within either a system jump or traveling between planets), Joker will say something along the lines of "receiving a message from... guess who... again..."
When Shepard first wakes up in the Lazarus Research Station and is following Miranda's directions, s/he runs across a staff member trapped in a burning room with a YMIR Mech bearing down on him. The man sees Shepard and calls out for help. However, if an Infiltrator Shepard activates Tactical Cloak before entering the man's line of sight, he won't call for help; he'll just yell as the mech kills him.
If you walk into the opposite gender's bathroom, EDI calls you over the intercom to remind you the correct one is on the other side of the ship.
If you played the first game and purposely missed recruiting Garrus, Shepard will have special dialogue when Archangel takes off his helmet. Granted, it's a one-line change, but it's still significant.
When recruiting Archangel, if you stand in the way of his shots, you get hit exactly once, just enough to bring down your shields. Shepard can stand there all day and not get hit again, even while mercs drop like flies around him/her. Garrus even comments on this later.
Most characters that are only recruitable after Horizon have dialogue in the game for missions beforehand, even though they are impossible to obtain legitimately and can only be experienced by altering a save file. Examples include:
On Mordin's recruitment mission, you can hear Samara and Thane begin to succumb to the alien plague. (Tali is unaffected due to her suit).
All squad members have dialogue for Jack's recruitment mission, regarding the prison's use of torture.
Legion is a very interesting case - they can only be recruited near the endgame, yet there are special dialogues and events for almost the entire game. The most interesting case is the cut dialogue on Korlus. If you have Legion in your party, they will talk to Rana Thanoptis, a character who (depending on your choices) may or may not have survived the first game.
When Shepard first meets Grunt, s/he has the option to shoot him a few times to get the point across that Shepard is in charge. If the option is taken, Grunt is shown bleeding from a bullet wound in the mouth afterwards. If Shepard leaves the room and comes back, Grunt will still have this wound on his face in subsequent conversations, though it goes away once Shepard leaves the engineering deck.
In Zaeed's loyalty mission, in his rage to get Vido, he triggers an explosion that threatens to burn hundreds of innocents alive. Paragons go through the facility to stop the fire, allowing Vido to escape, but the fire traps Zaeed under some rubble. If you perform this mission after the Suicide Mission - after Zaeed has fulfilled his contract - you can opt to leave him there to die.
The easiest way to get into Hock's room during Kasumi's loyalty mission is to tell the guard you have clearance from one of his superiors. However, if you can't find his captain's name, there's a route for you to climb down the terrace and break in through some windows. That's not this trope. The development team thinks of everything regarding an alarm clock you can set off in Hock's room. If you set it off when you lie to the guard, nothing extra will happen. However, if you broke in, the guard and another merc will come in, saying you're not supposed to be in there, prompting a brief firefight.
One of the first shops you encounter when entering the Citadel is the gift shop. Shepard can use a paragon dialogue choice to ask if "former Spectres" get a military discount. That is, unless you were reinstated as a Spectre prior to entering the shop by talking to Councillor Anderson.
When you walk up to the dragon's teeth on the Derelict Reaper, you get a brief exchange if your party includes someone who's seen them before - Garrus, Tali or Jacob (he was on Eden Prime). Miranda and Thane have extra dialogue at this point, but don't trigger the scene by themselves.
Earth's Council Representative comments on how no one seems to care you're walking around with a geth on the Citadel while random asari are being held for extended periods of time to make sure they're not working with the geth.
Taking Legion along to Tali's recruitment mission (where you fight other geth) has the effect you'd expect: Kal'Reegar warns Shepard that there's a geth behind him/her and Tali even shoots at Legion unless a Paragon interrupt is used.
Attempting to enter the quarian flotilla with Legion initiates a conversation that can get you kicked out without enough charm/intimidate points.
Talking to the attendant at the Wards Access C-Sec Office with Legion in your party will net some funny dialogue about infiltration risks from geth.Legion actually appears to be a bit offended, as he protests "Geth do not infiltrate." At this, the C-Sec officer will comment that Shepard should leave his/her personal synthetic at home as they aren't allowed on shuttles anymore. Legion, obviously mildly surprised that he was mistaken for anything other than geth, notes that "...geth do not intentionally infiltrate."
Taking Tali along on Legion's loyalty mission will net some interesting dialogue, arguments and casual banter between the two, regarding the geth's creation and the Morning War.
If you bring Legion with you on the Overlord missions, Archer asks you if he can be trusted.
Throughout most of the game, if you try to ask EDI questions about Cerberus, such as their resources or how they built the Normandy SR-2, she replies that a block has been placed in her systems that prevents her from answering. After Joker gives her full control of the ship because of the Collectors invading and kidnapping the entire crew, she can answer those questions if you ask her again.
Every squadmate has unique comments for each hub world (Omega, Illium, Tuchanka, and the Citadel). Interestingly, depending on the circumstances, the other squadmate may also have responses to the first one's line. A few examples:
(On Tuchanka) Jacob: These krogan never die. In the face of all this, they just keep going. (if Grunt is present)
Grunt: That's what we do: stay alive no matter what. No matter who.
(if Mordin is the other squadmate)
Mordin: Yes, problematic at times. Hypothetically.
Jacob: Wish I had that kind of stamina. Glad I don't need it.
(On Tuchanka) Legion: The krogan chose to bomb their own world into this condition. The creators were not so aggressive during the Morning War. (if Tali is the other squadmate)
Tali: We expected to get our worlds back! We didn't want to destroy them. Legion: We are glad you did not. You could not endure the conditions krogan thrive in.
(if Grunt is present)
Grunt: I don't expect a machine to understand. Or any alien. Legion: We stated historical facts. Perspective cannot alter them.
Lair of the Shadow Broker:
When you speak to Spectre Tela Vasir early on in the mission, part of her dialogue depends on your status. If you didn't save the Council and recommended Udina as a Councillor (the only way to not be given the opportunity to be reinstated as a Spectre) she calls it a pity.
If you chose to romance Liara in the first game, then romanced a different love interest in 2, Liara will call you out on your infidelity if you attempt to justify getting back together with her.
The first instance of Shepard's service history netting unique dialogue, which occurs after the confrontation with Tela Vasir. If you have the Sole Survivor history, she will call you out on working with Cerberus despite them gunning down the rest of your unit on Akuze years earlier.
Depending on which squadmate you brought, the Broker will comment on them, including your DLC characters (if you downloaded them). He will also express disbelief at "Samara's" (Morinth's) "changed agenda" (if you brought her), implying that even he is unaware that she assumed her mother's identity.
The Broker knows if you haven't finished your squadmates' loyalty missions. If you bring along Samara before you finish her loyalty quest, the Broker will express surprise that you haven't finished "her business on Omega". If you've found Kasumi (but haven't done her loyalty mission yet), the Broker says that she's "going to miss Hock's party". If you did complete her loyalty mission, he knows whether or not she's kept the graybox.
The Shadow Broker himself changes his stated goal when you confront him. If you haven't taken out the Collectors' base by that point, he'll say he will sell Shepard's body to the Collectors. If the base is captured, he will say he is after Normandy's Reaper IFF in order to salvage the base, or its debris if it was destroyed.
Liara is a playable character for this mission. For everyone else you have to complete their loyalty mission to unlock their powers. She is already fiercely loyal to Shepard so she already has all of them available.
Liara's dialogue when she visits Shepard's cabin will change depending on who you've romanced, whether or not you've completed the suicide mission, as well as depending on who you were able to save.
If you let the countdown timer run down to zero right after you wake up (which means waiting two real-time hours) or after the confrontation with the indoctrinated Kenson, a special Game Over vision plays that includes the crashed Normandy (with Shepard's helmet on a pike in the foreground) and the rest of the team standing together (along with the Illusive Man) as the Reapers invade Earth. The timer counting down will also be higher if you haven't finished the suicide mission.
The hologram during the final conversation with Harbinger will be different depending on if you've finished the suicide mission. If you haven't, the hologram will be of the Collector General. If you have, it will be of Harbinger's true Reaper form, similar to the conversation you've had with Sovereign on Virmire in the first game.
The final dialogue with Admiral Hackett changes slightly depending on whether you've completed the Suicide Mission, as well as what choice you made at the end. For instance, if you blew up the Collector base, when you comment on how odd it is for Hackett to willingly set foot on a Cerberus vessel, he adds the line, "Besides, I'm not really sure this is a Cerberus vessel anymore."
Sending a probe toUranus will make EDI reply with an exasperated "...Really, Commander?" Do it again and she deadpans, "Probing Uranus." The resources of the planet are also stated to be depleted, meaning the only logical reason you'd scan it is for the laughs. Though, in practice, there are actually often one or two mineral deposits on the planet, seemingly daring the player to launch a probe.
If you chatted up Barla Von, a very minor NPC whose sole purpose is to give you a lead at the beginning of the first game, he'll greet you amicably when you meet him again for another minor sidequest in the third game. If you never spoke to him at all, he'll introduce himself to you as if you never met.
The memorial wall on deck three of the Normandy automatically updates to add crew and former crew who die in 3, such as Mordin in one ending of "Priority: Tuchanka", and Thane after he is mortally wounded by Kai Leng during the Cerberus coup attempt. It also has anyone who died during the suicide mission in 2, as well as everyone who died during the Collector attack which destroyed the SR-1, but only if their dogtags where collected at the Normandy's crash site.
Completing the ME2 DLC Lair of the Shadow Broker opens up several additional dialogue options and conversations:
If Liara and Garrus are brought on the Priority: Sur'kesh mission, they will have extra dialogue playfully reminding her of the fact that the previous Shadow Broker was a yahg, and the one that just escaped its holding cell could be the next one.
Shepard: Careful. There goes the next Shadow Broker. Garrus: Could've sworn it was muttering "T'Soni!" the whole time. Liara: Not funny!
Watching the terminals in the Shadow Broker base in 2 will mean that during the conversation with Matriarch Aethyta, Shepard informs her that they've seen footage of her looking at a picture of Liara and politely tells her to cut the crap, since it's obvious that she's Liara's father.
If the player takes Liara on the Geth Dreadnought mission, she will mortify Tali by revealing that she's aware Tali's suit is equipped with a NerveStimPro Program... the Deluxe Edition.
The Shepard VI you encounter is a caricature of your personality in Mass Effect 2. If you played Paragon, s/he'll say uplifting heroic things. If you played Renegade, s/he'll talk about kicking ass and ask to be installed in various mechs and weapons.
In the "Grissom Academy: Emergency Evacuation" mission:
If the player is using a female Shepard who is currently in a romance with Garrus, Jack's dialogue will change after Garrus sarcastically calls Jack "as charming as ever" (this is after Jack greets Shepard by punching him/her in the face and berates him/her for having trusted Cerberus before). By default, Jack will greet Garrus by telling him that his "face still looks like shit." But if Shepard is female and has romanced Garrus, Jack will snap, "Bite me, Garrus! Or better yet, bite her! Probably how she likes it!" There are no other romances that change Jack's dialogue.
If Jack did the barrier at the Collector Base, she says she tells the tale of her feat as motivation to her students during endurance exercises.
Jack: I kept thinking to myself: 'Damn, let the salarian handle this!'. He could talk 'em to death.
If EDI is one of your squadmates, and if you rescued David Archer from Project Overlord, David recognizes her as the Normandy ship's computer and says that he's "sorry" for having tried to hijack her before. EDI says no apologies are necessary.
When talking about his exploits with James Vega, Garrus's dialogue will be different if you didn't recruit him in the first game.
Delay talking to Garrus after recruiting him, and when you finally head down to the Battery, he'll comment that he was beginning to think that Shepard had forgotten his favourite place on the ship.
In the second game, if you talked to Mordin enough, you'd hear him sing an odd version of Gilbert & Sullivan's "I Am the Very Model of a Modern Major-General" with salarian-appropriate lyrics. In 3, if Mordin makes the ultimate sacrifice on Tuchanka, you'll hear it again — but only if you heard him sing it in the previous game.
If you choose to sabotage the genophage cure on Tuchanka, if Wrex is alive and you completed his family armor quest in ME1, Wrex will reference the latter mission while asking why you betrayed him in Citadel Docking Bay 94.
During the Citadel Coup, if Shepard can't bring Ashley/Kaidan around and hesitates to shoot them when it becomes necessary, a squadmate will take them out instead. The game keeps track of who it was, and gives them new after-mission dialogue reflecting this.
If Tali was sent through the vents in the Collector Base in the previous game, dialogue will occur with her complaining about having to go through more vents during the mission on the Geth Dreadnought, as well as grumble about what happened last time.
Tali: I got set on fire!
If a Male Shepard romanced Tali in the second game, during the Geth Dreadnought mission, they will constantly flirt with each other. When Tali saves Shepard from the collapsing lift, she has a Tsundere reaction to Shepard's joke that she was clearly worried about him. Depending on the third squadmember, EDI will explain to new squadmates that Shepard and Tali started a sexual relationship in the previous game, while if Garrus is on the team, he mentions he was there when they had their thing and says that the two should just get a room already. The Virmire Survivor will also be completely unfazed by the revelation, as though they were expecting it to happen.
If Legion's loyalty mission was completed, Shepard & Joker will make a Call Back to the "Geth don't use windows" discussion during the Geth Dreadnought mission.
Admiral Raan will be understandably freaked out when Legion arrives in The War Room unless you brought Legion to Tali's trial in the previous game, in which case she responds, "I see your geth friend has returned."
If the Rogue VI mission was completed in [ME1], EDI will have additional dialogue referencing her development from the program while bypassing one of the doors in the Priority: Cerberus Headquarters mission.
If Shepard never talks to James Vega in the ship throughout the game until the finale, he'll actually be pretty angry about being ignored. You will also get different lines depending on when you speak to him - waiting until EDI acquires a new body will lead to a discussion of that before sparring, for example.
During the Conduit Run, after getting shot by Harbinger, if you go to the squad screen — which is highly unlikely, as you have no reason to level up any more — Shepard's armor is the burned version s/he's currently wearing. You'll also notice that Shepard has no shield stat, or even any of the stat bonuses that the armor granted.
If the player interacted with Harrot (and obtained a discount) in ME2, Harrot will have extra dialogue mentioning that Shepard looks familiar, and Shepard will remark briefly on their prior dealings.
The first instance in the series where a new plot option becomes available depending on your class and not your background or accomplishment, during the sequence to disable a force field, where taking the Renegade interrupt to overload it will kill thousands of innocent civilians. Aria keeps telling you to go for it, but you then have the option of ignoring the Renegade interrupt three times so you can simply re-route the power instead. If you do that, Aria berates you for putting her and Nyreen Kandros' lives at risk. However, if Shepard is an Engineer, a Paragon interrupt allows Shepard to re-route the power without killing people right away, so Aria won't scold you for taking so long that her life was at risk.
There are two instances where a Shepard with biotics will use those abilities in cutscene - a scripted quick kill from behind cover at the start of the DLC, and a renegade interrupt to block a biotically charged attack at the start of the battle with the Shepard clone. The clone will also use biotics to knock Shepard's weapon out of his/her hands, as opposed to shooting it out like the other classes.
When Shepard is rescued by their squadmate near the beginning of the DLC, all five potential rescuers will use a character appropriate means of taking out the mooks they're fighting. Ashley and Garrus simply shoot them as would be expected, Kaidan and Liara will use their biotics, and Tali will zap them with her Omni-tool.
Engineer Shepard has unique lines during the casino infiltration, with Brooks even admitting that she'd momentarily forgotten that you probably know at least as much about spoofing security as she does.
The Big Bad is a clone of Shepard. Whose class and face will correspond with that of the player's Shepard. This is notable in case of the face, because you'd perhaps think that the game just uses Shepard's face code to determine how the clone will look. It doesn't. Even a modified Shepard, with hair not available through normal means for example, will be looking at a direct copy of themselves.
In the final battle of the DLC, the clone will be wearing standard N7 armor, just like what Shepard starts the second mission withnote Unless doing New Game+, when Shepard will start the second mission with whatever armor the imported save had set to equip. and is featured with in all of the game art. However, if the player has Shepard wear his/her own standard N7 armor, the clone's armor will have a blue marker beside the N7 logo and a blue stripe on the right arm instead of the details being red, like Shepard's. Because the clone and Shepard are identical in appearance, even with mods, this allows the player to tell the two apart in the action-heavy cutscenes. Becomes a good example of Gameplay and Story Integration and Fridge Brilliance when you realize that without that color difference, both Shepard's squadmates and the clone's henchmen wouldn't know who to shoot at during the firefight, or know who to save when both Shepards end up dangling from the edge of the cargo bay door. The color change only occurs when Shepard is wearing the completely default armor, down to detailing and color choices.
When choosing companions just before the "Retake the Normandy" section, the companion that has been used most throughout the gamenote Of the ones being left behind will say they wanted to go, while the squadmate that was used least will complain about never getting picked.
When you arrive to the captured Normandy, your teammates will open the door by hacking it with an omni-tool. Unless you took Wrex and/or James, in which case James will kick the panel or Wrex will shoot it. Immediately after, when discussing how to get the emergency hatch open, Kaidan, Liara, and Javik will mention the possibility of using a biotic field but not having the necessary fine control, while everyone else will just say that a very precise mass effect field might work.
If Garrus was brought during Mordin's loyalty mission from the previous game (during which he makes a comment about it being fun to have a firefight in an antique shop... "but only if it's classy"), and if he's brought up on the "Retake the Normandy" section of the main mission, he will reference the same dialogue during the firefight in Normandy's CIC.
If Wrex and Ashley/Kaidan are Shepard's squadmates on the "Retake the Normandy" section, and if they had the "Who would win in a fight?" conversation on the elevators back in the first game, Wrex will reference that conversation (while on the elevator down to the cargo hold, no less!), saying that they're finally about to get an answer.
In the Normandy elevator, if the Lair of the Shadow Broker DLC was completed and Liara had the discussion with Aethyta, and if Wrex is also present, she will remark on the fact that she is technically part-krogan and Wrex commenting with approval.
When meeting with Jacob at the Castle Arcade, a female Shepard who romanced him in the previous game can be hostile towards him over their broken relationship. If Shepard romanced Kaidan or Liara in Mass Effect 1, Jacob will call her out on it.
Depending on the type of party Shepard throws, James and Liara can be found bickering over biotics being better than sheer physical strength. If Kaidan and Jacob (who are also biotic and account for all three biotic classes when counted with Liara) are alive, they'll throw in their two cents. Jack or Miranda will also be present if the other one is not, and a biotic Shepard will bring up his/her status as a biotic as well.