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..."
Listen to the conversation between the elcor ambassador Calyn and Xeltan. They don't preface their words with their emotion. Why? They don't need to. They only do that with non-elcor who can't detect their odors and subtle movements to derive emotional subtext.
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 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.
In the Lair of the Shadow Broker DLC, the Broker will comment on your squadmate - 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.
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.
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.
Legion is a very interesting case - they can only be recruited near the endgame, yet there are special dialogues and events for bringing them on a ridiculous amount of missions. Even more interesting is that the character cannot be used before the second set of missions, because of development changes (meaning that most of its dialogue cannot be accessed through normal gameplay - you have to mod the game to get the character earlier.
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.
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.
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.
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.
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.
On Mordin's recruitment mission, the entire roster of squadmates has dialogue when they exclaim that they've been afflicted with the virus. (Unless you take humans, or Legion - as they are immune, or Tali, whose airtight suit is specifically designed to prevent infection).
In the Arrival DLC, if you let the countdown timer run down to zero right after you wake up (which means waiting two real-time hours), 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."
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.
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.
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.
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.
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 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.
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.
When you speak to Spectre Tela Vasir in the Lair of the Shadow Broker DLC 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.
An meta example goes out to the game itself, specifically the PlayStation 3 version. At the time ME2 was released, there was no PS3 version of ME1. Even with the Cerberus pack, with the comic that lets you pre-select many of the major decisions from the first game, there are many, many other decisions and quest outcomes that didn't get ported over. Nonetheless, the developers made sure to include them, and with the online release of the original game, PS3 owners can see those added extras for the first time.
If you bring Legion with you on the Overlord missions, Archer asks you if he can be trusted.
If you walk up to a medical bed on Freedom's Progress, it'll show a little hologram of your skeleton. That's some pretty impressive attention to detail.
Everything is tracked. Word of God is that more than a thousand save-game flags are tracked from the first two games and imported into the third. Everything from the obviously major to the absurdly minor is noted. For example, 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, when you meet him again for another minor sidequest in the third game, he'll greet you amicably. If you never spoke to him at all, he'll introduce himself to you as if you never met.
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 just goes "I see your geth friend has returned."
If Tali was sent through the vents in the Collector Base at the climax of Mass Effect 2, dialogue will occur with Tali 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 Legion's loyalty mission was completed, Shepard & Joker will make a Call Back to the "Geth don't use windows" discussion during the same mission.
If a Male Shepard romanced Tali in the second game, during the Geth Dreadnought, they will flirt with each other throughout the mission. 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.
Likewise, 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.
In the second game, if you talk to Mordin enough, you'll 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 Mass Effect 3, if Mordin makes the ultimate sacrifice on Tuchanka, you'll hear it again — but only if you heard him sing it in Mass Effect 2.
If you speak to Mordin in his lab, they have a conversation about his plans to retire to the beach and collect seashells. Shepard jokes that he'd clearly get bored within minutes, so Mordin ponders about perhaps running tests on the seashells? The game then adds new dialogue as a Call Back later on Tuchanka, where Mordin will comment before his Heroic Sacrifice:
Mordin: Pity. Would liked to have run tests on those seashells...
If Shepard never talked 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 standoff on the Citadel, 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.
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 hadn't forgotten his favurite place on the ship.
Unlike in 2, Shepard can only enter the bathroom belonging to their gender. Presumably, EDI got tired of reminding them they were in the wrong bathroom and automatically locks the door.
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.
If the player has completed the Lair of the Shadow Broker DLC in the second game and takes Liara to the Geth Dreadnought, Liara will mortify Tali by revealing that she's aware Tali's suit is equipped with a NerveStimPro Program... the Deluxe Edition.
Watching the Shadow Broker terminals 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.
During the very last section, 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.
If, in the first game, you hung up on the Council at least once, Joker mentions it at least twice, once to Shepard after you've talked to the Council, and once to Liara in her quarters.
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.
On the same mission, 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.
In the first instance in the entire series where a new plot option becomes available depending on your class and not your background or accomplishment, during the Omega DLC, you are trying to disable a force field but 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.
If you didn't complete the Lair of the Shadow Broker DLC in the second game, there's a scene where you talk with EDI about the human perspective, and Shepard wants to know why she doesn't go for, say, the asari perspective. EDI responds that Liara doesn't trust her as she is a "blabbermouth". EDI then complains that Liara has gotten more secretive since becoming the Shadow Broker. To which Shepard responds "Wait, Liara's the Shadow Broker?"
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 at the start of ME2 which destroyed the SR-1, but only if their dogtags where collected at the Normandy's crash site.
When talking about his exploits with James Vega, Garrus's dialogue will be different if you didn't recruit him in the first game.
The Big Bad of the Citadel DLC? 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 Citadel DLC, 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.
Depending on the type of party Shepard throws in the Citadel DLC, 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.
When meeting with Jacob at the Castle Arcade, a female Shepard who romanced him in Mass Effect 2 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.
When choosing companions at a certain point in Citadel, 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 Shepard is rescued at the beginning of Citadel, 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.
When you arrive to the captured Normandy in the Citadel DLC, your teammates will open the door by hacking it with an omni-tool. Unless you took Wrex and/or James, in which case one James will kick the panel, or Wrex will shoot the panel. 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.
It is not possible to take both Ashley and Kaidan with you in Mass Effect 3, because of the Virmire decision. However, they are separate characters within the game, so if the save game is edited, both characters can be selected without the game crashing, they occupy different spots on the character select screen, and will converse with each other. Almost as if the devs knew some players would hack them both in.
In the first game, there were originally going to be romance options between Male Shepard and Kaidan, but they were removed. However, the data still exists in the game. Fans being fans, a mod was made to put it back into the game proper. If you happened to use that mod, then in the third game, the dialogue between Kaidan and Male Shepard will be altered, to reflect the fact that they've been in a relationship.
The Citadel DLC will give an Engineer Shepard 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.