The Dev Team Thinks of Everything/Mass Effect

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.
 * In 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 people don't even know the option is there to run from that encounter.

"Garrus: That's unfortunate - hospitals aren't fun to fight through. Shep: What is fun to fight through? Garrus: Gardens, electronics shops. Antique stores, but only if they're classy."
 * In Mass Effect 2:
 * If you played the first game and purposely missed recruiting, Shepard will have special dialogue when takes off his helmet. Granted, it's a one-line change, but it's still significant.
 * There are many situations where bringing two specific squadmates on certain missions/making decisions in the first game will net unique dialogue (both in cutscenes and in-game conversations). Some of the major instances include:
 * On Tuchanka, bringing Miranda on Mordin's loyalty mission will result in special dialogue where she says she's made a note of Shepard referencing Cerberus during a cutscene. Bringing Tali results in her getting offended when you tell the sickly Krogan hostage that he should stop acting like a whiny Quarian. Bringing Grunt along on Mordin's loyalty mission will net extra dialogue regarding the Krogan genophage. Bring, and she makes a comment to Mordin using her actual voice (the only time she ever speaks this way to any crew member in the game). Taking Garrus on Mordin's mission results in him saying one of the most Badass things in the entire game:


 * Bring Zaeed along during Tali's recruitment mission, and during the battle with the Geth Colossus, he'll spontaneously shout that he'll be getting extra pay for "anti-armor duty"! Grunt will exclaim "This is why I follow you, Shepard -- BIG THINGS!" Kasumi gets a Shout-Out to Godzilla: "Oh God - COLOSSUS!"
 * If you take Miranda in your final party when you go to destroy the Human Reaper, an alternate cutscene plays as you arm the device to destroy the Collector base. The Illusive Man orders Miranda to stop Shepard, and she states that she knows she'll just be a liability to Cerberus at that point, before giving her resignation. In the third game, Miranda will have left Cerberus whether you triggered this cutscene or not.
 * 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 "changed agenda" (if you brought her), implying that even he is unaware that.
 * 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".
 * is a very interesting case - can only be recruited near the endgame, yet there are special dialogues and events for bringing  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  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 on the Citadel while random asari are being held for extended periods of time to make sure they're not working with.
 * Attempting to enter the Quarian flotilla with initiates a conversation that can get you kicked out without enough charm/intimidate points.
 * Taking along to Tali's recruitment mission (where you fight other ) has the effect you'd expect: Kal'Reegar warns Shepard that there's a  behind him/her and Tali even shoots at  unless a Paragon interrupt is used.
 * The most interesting case is the cut dialogue on Korlus. If you have in your party,  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 in your party will net some funny dialogue about infiltration risks   actually appears to be a bit offended as he protests  at this the C-Sec officer will comment that
 * Sending a probe to Uranus will make EDI reply with an exasperated "...Really, Commander?" Do it again and she deadpans, "Probing Uranus."
 * Remember how Collector technology lets them see through the Normandy's stealth systems? During the fight with the Oculus during the Suicide Mission, it can see through the Infiltrator's Tactical Cloak.
 * Actually, the Normandy's stealth systems only hide it from sensors. Even if they're all on, it'll be visible if you just look out a window.
 * 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.
 * The game designers originally planned for the player to recruit any of the squadmates at any time. Modding the game to bring certain characters on the early missions gives you alternate cutscenes and dialogue that aren't accessible any other way, but were programmed in:
 * 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 - as they are immune or Tali, whose suit completely completely covers her).
 * 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 timer counting down will also be higher if you haven't finished the suicide mission.
 * 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."
 * 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, she can answer those questions if you ask her again.
 * 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.


 * In Mass Effect 3:
 * 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 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."
 * One sidequest involving Running Gag character Conrad Verner is practically a checklist of a bunch of things that you did in the first game. He has different dialogue depending on whether or not you hit him or shot him in the foot in the second game, if you found all of the Matriarch Dilanaga writings, if you recovered some data discs for another minor character on Feros, and the entire quest will change completely if a seemingly unrelated other minor character was helped or ignored in the first game. He even lampshades an import bug related to whether you handled him Paragonically or Renegadeishly in Mass Effect 1.
 * 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. 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.
 * 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.
 * 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, you'll hear it again — but only if you heard him sing it in Mass Effect 2.
 * In the Play Station 3 release of Mass Effect 2, Conrad Verner assumes you went with the Renegade option and stuck a gun in his face in ME1 (since ME1 never got a Play Station 3 release, though this happens in all versions of the game). If you take the Paragon option with him in 2 and meet up with him again in 3, he'll apologize for saying that, since he was under a lot of stress at the time.
 * If Shepard never talked to James Vega in the ship throughout the game and only talked to in the finale, he'll actually be pretty angry about being ignored.
 * The Shepard VI you encounter in Mass Effect 3 is a charicature of your personality in Mass Effect 2. If you played Paragon, he'll say uplifting heroic things. If you played Renegade, he'll talk about kicking ass and ask to be installed in various mechs and weapons.