Tali's loyalty mission ends with her either taking the blame for her father's crimes and being banished, or you revealing her father's guilt and alienating her. However, if you have enough Paragon or Renegade points or saved both Veetor and Kal'Reegar, you can call the admiralty board's trial a sham, exonerating Tali and keeping her father's guilt hidden.
The confrontations between party members such as Jack and Miranda or Tali and Legion. Don't want to favor one companion's loyalty over another? There are alignment-dialogue options for that.
If Zaeed Massani's loyalty mission is done after the Suicide Mission, you can let Zaeed burn to death instead of earning his loyalty through standard means.
Take My Hand: Near the end, there is a scene where one of your party members slides off a falling Collector platform, leading to Shepard saving them in this manner. Twice. Shepard is also rescued this way about 45 seconds later.
The video game salesman on the Citadel has a lot of these, including what may be a dig at EA for their DRM when he informs the player of a special warranty that lets you re-download a game if its copy protection corrupts it. With EA's then-current DRM problems with Bioware's Dragon Age: Origins, it takes on a Harsher in Hindsight quality.
Quite a few salesmen have those. The Saronis Applications clerk has this jab at audiophiles and their expensive cables:
Marab: It's stunning how many people think that light moves faster through expensive fiber optic cables than it does through cheap ones.
There's also a few aimed at fans. For instance, on Illium you can find a quarian girl in a bar complaining to her (friend-zoned) turian co-worker about how it's always the same thing when she's dating a human: "Oh, she's vulnerable! She could get sick! I wonder what she looks like under the helmet!" Bring Tali with you for maximum awkwardness!
An asari on Illium is quick to point out that she doesn't trust humans with anything, after all, "You can't even figure out your own religions!" Ouch.
If you ran into a few cars in the Lair of the Shadow Broker DLC, you'll comment about the bad controls. Liara will comment about how it's still better than the Mako.
Take Your Time: Subverted. If you don't immediately go through the Omega-4 relay after the Collectors abduct your crew, you'll find a lot less of them alive, and one of the survivors chews you out for dragging your feet. Played straight at every other point in time, except at a few points where the next story mission is literally forced on you. Which might be why the subversion is so devastating.
The point where Take Your Time stops being a factor coincides with when Shepard goes from being reactive to proactive. It's also implied that the preparations for the Suicide Mission actually take several months.
Talking Is a Free Action: Played straight in most cases, but averted in some. QTE cutscenes interrupt talking on a regular basis. Ditto any time Harbinger possesses a Collector — a good weapon and a fast shot can nail him before he's finished his speech.
Teeth-Clenched Teamwork: There were certainly awkward moments between squadmates in the first game, but the second features people actively trying to kill each other. Not one person in the whole group completely trusts everyone else. Except (possibly) Shepard. Not until the end, at least.
Garrus: You know me. I always like to savor that last shot just before popping the heat sink. Beat Garrus: Wait... That metaphor just went somewhere horrible.
That Was the Last Entry: A few times, but the most heartbreaking example is probably from Samara's loyalty mission — Nef's last journal entry before she goes to meet with Morinth.
The Bad Guy Wins: A bit of a meta example if you get the worst ending where Shepard dies and spares the Collector base. Since The Illusive Man turns on Shepard in the third game it's essentially killing two birds with one stone.
Most weapons inside of their families. The most prominent example are shotguns, which are named after swords (Katana, Scimitar, Claymore; DLC Eviscerator).
Several planetary systems have theme names. Whether they're all given names in alien races, or they're all named after afterlives in Earth religions (go to the Exodus Cluster in the first game to see) or they're all named after characters from the Old Testament; there's also a cluster with all the systems named after physicists, and one system where all the planets are biologists.
The Widow, full stop. A few seconds reading the description of the Widow will reveal that it's an ANTI-TANK rifle. Since you're using a rifle designed to destroy armored vehicles and krogan, on people with regular armor, it's not hard to see how this trope applies.
The Cain isn't a nuke launcher, but it may as well be. On lower difficulties, it can almost take out the Final Boss in one hit.
Clan Urdnot protects their food stores from pyjaks (little furry critters that resemble purple chimpanzees) with an artillery cannon. At the player's discretion, Shepard can point out how absurd this is. Garrus also takes note of this.
In the Suicide Mission, disabling the Collector's vents before your tech specialist is roasted alive. Also, technically the Final Boss, as the longer you take to defeat it, the more likely at least one of your squadmates will be picked off.
The final parts of both the Overlord and Arrival DLCs are timed missions. Arrival specifically has several timers, starting at two days, then decreasing to an hour and a half, then five minutes. And if you wait around long enough, they dorun out.
Also the sidequests dealing with the launched Javelin missiles and saving the falling ship by re-activating its engines.
Tomato in the Mirror: Seems to be subverted and played with, as people expect Shepard to be one of these, considering the game picks up two years after their death on the Normandy and subsequent rebuilding by Cerberus. One dialog path has Shepard think of this as soon as they finds out.
Too Awesome to Use: Higher-end heavy weapons. As heavy ammo doesn't, normally, fill between missions and cannot be purchased at any in-game store, a player usually has a limited amount of heavy ammunition available throughout the game.
Not to mention the fact you can choose not to use them at all and get more credits every time you find a heavy ammo pack out in the field. Not a great deal (100 credits), but it adds up.
Basically you will only use heavy weapons twice in the game: on Grunt's loyalty mission (the Thresher Maw) and against the final boss (the only time in the game where heavy weapon ammo spawns outside of fixed containers). On a higher difficulty, Horizon's final boss, the Praetoriannote although you'd better make sure you're damaging its armor and not the barrier which occasionally regenerates when you're too close to it may also qualify. Any other time: save that ammo.
Special mention should go to the warden of the Purgatory, who thought that trying to take Shepard prisoner to ransom them, both angering the Commander and betraying the Illusive Man, was a good idea. Not only that, but he lets your party keep your guns when you board.
The merc leader at the beginning of Miranda's loyalty mission. After all his talk, a Renegade interrupt will result in Shepard grabbing him and snapping his neck, as they and Miranda take out three other mooks nearby.
Go ahead. Sleep with Morinth.
Elnora from Samara's recruitment mission tries to shoot you if you did the Renegade interrupt. She is one person who probably just killed once. You have two people with you, are heavily armed, and have something special about them. Guess how well she does against you and your squad.
Dr Amanda Kenson in the Arrival DLC. As Shepard themself mentions, leaving Reaper technology in an open space, uncontained and surrounded by security guards, is a very, very stupid idea.
Also, Zaeed can relate a story about how smoking can kill you... apparently, a kid he knew decided to toss a butt near an explosives cache.
In Grunt's loyalty mission, Uvenk tries to kill Shepard, Grunt and their squadmate after the three of them survived against or killed a Thresher Maw.
Admiral Rael'Zorah and the entire research team in Tali's loyalty mission. They were experimenting on geth parts to design better weapons against them. What did they do? They deliberately allowed every geth to be part of a network even though they knew geth grow far more intelligent when more of them are networked together, they had absolutely no low tech way of handling the threat of the geth taking over such as a simple bomb, when their computer network was slow they deliberately took down the firewalls to speed it up while the geth were fully networked and did all this on a ship with weapons. If not for the very fortunate actions of one of the researchers probably far more quarians than just the ones on the ship would have been killed. Note that the ship was still with the Migrant Fleet the whole time.
Took a Level in Badass: The Colossus. Remember hunting those tanks down for experience in the first game? In the sequel there is only one, in Tali's recruitment mission. You fight it on foot, and, thanks to its fire support, it can wipe the floor with you if you choose a wrong path.
Similarly, the thresher maws in the first game weren't a tenth the fight as the one in the second, during Grunt's Rite of Passage.
Total Party Kill: The absolute worst ending. You do kinda have to work to get it.
Tragic Villain: The Collectors are completely controlled by Harbinger and the Reapers, even built by them — out of the Protheans.
Mordin: No glands, replaced by tech. No digestive systems, replaced by tech. No soul, replaced by tech.
Transhuman Treachery: Averted through most of the game, but played with in the Overlord DLC: David Archer - the titular Overlord - hacks Shepard's implants in the final dungeon. Not for any purpose of sabotage, just the ability to give his side of the story.
Trash the Set: The game opens with the Normandy being destroyed. One part of the day-one free-to-new-copies DLC is a visit to the wreck of the ship, and it really exemplifies this trope, going as far as giving flashbacks to what each part looked like undamaged.
True Companions: Shepard's goal is to take their team and turn them into this. In addition, numerous responses from Paragon Shepard essentially boil down to "you're part of my crew." EDI even uses it to calm fears that she'll go 2001: A Space Odyssey on everyone after she's unshackled and merges with the Normandy. Also the only reason Joker doesn't get abducted by the Collectors, as the Normandy's crew buy him time to escape by fighting energy-gun-bearing Scions with small arms. Although the latter is also rational behavior: Joker is the only one who can activate the ship's security which would be the only way to really get rid of the attackers. It makes enough sense to protect him better than yourself, because without him, you're definitely toast.
Turtle Power: The krogan have beaks, shells, short stubby tails, and the longest natural lifespan among the space-faring races — in fact, Urdnot Wrex is over 1400 years old, well beyond the thousand-year lifespan of the asari. They are mentioned as being reptilian, and resemble nothing so much as anthropomorphic tortoises.
Tutorial Failure: The Firewalker DLC features on-screen tool tips that give the wrong keys for a number of necessary tasks to use with the Hover Tank (jumping and mining, specifically). This is presumably the result of a minor case of Porting Disaster.
Twin Threesome Fantasy: Seen on Kasumi's loyalty mission, an old human man at Donovan Hock's party has two matching asari on either arm.
Two Plus Two Makes Five: Basically, this is how the "heretic" virus works, by altering the geth's logic system to come to a different conclusion. In other words, an indoctrination virus. You are given the opportunity to turn their virus on them. Notably, this subverts the usual Black and White Morality of the Paragon/Renegade dichotomy, as the Renegade "kill them all" option can be justified as being more morally correct than brainwashing them.
The Unfought: Harbinger, sort of. While he takes over plenty of Collector drones to fight you, he never gets a proper boss fight in his true form or anything. Of course, that may be because he's hiding beyond the galaxy's horizon. And because he is a fully grown Reaper. The Collector General is probably a better example.
What happens with the Unity power, which allows Shepard to revive their squadmates if they fall in battle (and only then). Lampshaded by one of Garrus' responses to being revived:
Garrus: I'm better now.
If you import a Shepard who did Nassana Dantius's quest on the Citadel, she will be unbelieving that you're somehow alive again when you meet her again. Shepard will respond with "I got better".
Shepard can also quote this word for word to Liara in the Lair of the Shadow Broker DLC.
Unique Enemy: The Technician in Jack's recruitment mission, notable for two reasons: first, he's the only technician enemy in the game; and second, he holds the "honor" of being the weakest enemy in the game. Low health, low shielding on Hardcore/Insanity, no powers, and wields the weakest pistol in the game. Even on higher difficulties, if you don't want to waste your thermal clips on him, you can just walk up to him and punch him in the face a couple of times. Or let your squadmates handle him—it's entirely possible the guy will die before you even notice he's there.
Universal Ammunition: Justified, as the "thermal clips" are not actually ammunition, but heat sinks that are made to fit into all small arms. While it would make sense for the guns to have the option to wait for the thermal clips to cool down as opposed to being forced to eject the clip and insert a new one, the game doesn't give the option and make it impossible in-game. There's also the power cells, which any heavy weapon, from a flamethrower to an explosive lobber, can make use of.
Unperson: Tali states that if her father were found guilty of bringing live geth to the fleet, he'd be written off all Flotilla records and become a bogeyman used to scare children. Whether this happens or not is up to you.
Unreliable Expositor: The Codex, written by the Alliance and the Citadel. Especially unreliable with regards to anything having to do with Reapers.
The Unreveal: By romancing Tali, Shepard can find out what's under her helmet, but camera angles conspire to make sure that the player never does.
Unusually Uninteresting Sight: Should you choose to recruit Legion, a geth, you can take him anywhere with few reactions. Notably, you can take Legion to the Citadel of all places and nobody will object. Lampshaded by Anderson if you ask him about the war with the geth with Legion in your party. Subverted, of course, in the Migrant Fleet, where every quarian will have some degree of reaction towards Legion.
Unwinnable by Mistake: If you go around blowing money on probes and fuel, use them up, and carry on doing this until you've exhausted all the money that it's possible to earn in the game before the Reaper IFF mission, then there's no way you can get to the star system where that mission takes place, making it impossible to proceed in the game. Since there are a lot of credits in the game though (even without any DLC packs), it's pretty dang hard to actually do this, although enough first-time players reported having made the game unwinnable for Bioware to make sure it couldn't be repeated in Mass Effect 3, where you get free fuel refills whenever you visit the Citadel.
Used Future: Typically averted through the entire series, but played straight on Omega and Pragia. Omega is the series charging headfirst into Darker and Edgier territory, while Pragia (the setting of Jack's loyalty mission) has been derelict for several years.
Both the Bypass Module and Hack Module increase the amount of time you have to hack terminals and bypass locks respectfully. You already have plenty of time to do both without these upgrades and they also cost 30,000 credits each, so neither is worth the investment.
Of the 3 Instant Armor bonus powers, Grunt's Fortification is the only one that doesn't benefit from the Tech and Biotic duration and cooldown bonuses that Geth Shield Boost and Barrier receive. If you need one, pick from one of those 2 instead.
Values Dissonance: An in-universe example. On Illium, indentured servitude is legal. The player can meet an asari contract broker and a quarian who sold herself into slavery indentured servitude in order to cover a large debt she incurred playing the stock market. While the quarian is not happy about her situation, she is less upset about her status than with the financial troubles which led to this solution. The broker claims humans are prejudiced against slavery because of their poor experiences with batarian slavers, explaining the legal protections provided to indentured servants by their contracts, including strict limits on its length, the duties involved, and how they're treated. The asari representative that the slave was to be sold to, meanwhile, is initially unwilling to buy the quarian's contract because they're anti-slavery one of the few licensed AI-research companies, who have been suffering bad press following the geth attacks in the first game. (The Charm option can have you convincing them to pay the fine to break the contract and hire her as an ordinary employee, resulting in a PR boost.)
The asari contract broker also seems to be under the impression that Shepard's angry reaction is due to batarian slave raids on human colonies giving them bad ideas about indentured servitude and slavery. You have to wonder how the asari Contract Broker would react to learning the truth about the majority of humanhistory and why it's something of a sore spot?! Though if Shepard has the right background, it could be interpreted as a bit of both for him/her.
Vendor Trash: Completely averted. Unlike the first game, there is no inventory whatsoever, so there's nothing to sell. Most equipment is upgraded rather than replaced, and when a new weapon is obtained, it (usually) becomes immediately available to all characters who are capable of equipping it.
Vengeance Feels Empty: It is possible to convince Garrus of this through Paragon dialogue during his loyalty mission. Averted with Zaeed; even if you take the Paragon path and still retain his loyalty, he decides merely to put his quest for revenge on hold until the end of your mission.
Verb This!: Blasto the hanar Spectre pulls one of these. "Enkindle this."
The other side of the Omega-4 relay — the Collector base. Not only is it located in the galactic core, but you have to travel through a relay that's glowing red instead of glowing blue. Oh, and when you get there you can see the supermassive black hole that's in the very center of the galaxy in the distance. And don't forget the space full of wreckage from your predecessors.
In the Shadow Broker DLC, the Shadow Broker's lair counts as one, as it's the final location of the DLC and fits the criteria visually as well. It's a highly elaborate ship that floats in the clouds of the planet Hagalaz, complete with large amounts of lightning in the sky. Liara notes that the planet's conditions keep anyone from knowing the ship is there without previous knowledge, and must have taken decades to build without anyone noticing.
Considering you can potentially finish the game just fine without doing all the primary quests, but need to do so to ensure everyone survives the end, this game is pretty much entirely based around this trope.
Should we even get into minor quest characters and random overheard conversations on top of all of that?
This trope is probably best exemplified in-game by the Paragon interrupt at a certain poignant moment in Tali's loyalty mission. It would take a real stoic not to take that option if you know what that is.
It is possible to exact petty, satisfying revenge on those "monkeys" (known as pyjaks) that led you on a tedious chase all over the planet Eletania in the first game. The pyjaks are even explicitly mentioned to be stowaways from the very same planet. On the planet Tuchanka, pyjaks are infesting a settlement's food supplies, and you get to take down as many of them as you want. With a missile turret. For a shop discount and the gratitude of the local populace. Oh, and this time, you don't get Renegade points. So all you good guys of the galaxy, you go and have some fun, too. There's also a stray pyjak in Fortack's tent, which you can punch. You can only do this once, however.
There's also an achievement for watching ten enemies die screaming as they burn. The screams, it must be noted, are quite disturbingly realistic. (There's even a minor bug which turns up occasionally where the screams continue even after they're killed.) It makes for a very good strategy, though, because while they're running around screaming, they're not shooting at you.
In more psychological terms, you can break off a relationship with a party member at any point - including moments before the two of you would otherwise do the deed. Their reactions vary; Garrus mumbles something about how you're right and that you two shouldn't risk damaging your friendship, while Tali just says "Oh" before rushing out of the room. Kelly tells you that having a one-night stand with Jack is a bad idea, but you can still go ahead and do it, and thus use her like everyone else.
"Good thing the Reapers are coming to save the galaxy from this particular Shepard."
If you take your time with opening the heat exchange valves in the ventilation tubes while your tech specialist is crawling through them in the last mission, their pleas for you to hurry up will get increasingly... desperate. This leads to a Non-Standard Game Over if the player runs out of time.
In a very subtle example, Kasumi comments on how it's nice that she doesn't have to travel in a cargo hold and has an actual window to look out of for a change. You can close the blast shield over said window with a conveniently placed button, which has no function or purpose other than to enable you to make her room a whole lot more gloomy and bleak.
Fail to get the loyalty of a squadmate like Thane or Tali (by allowing his son to finish the job, or revealing the truth about her father) and see them becoming absolutely crushed. Thane becomes an even darker Death Seeker and Tali feels completely betrayed by someone she considered a close friend and mentor.
Tali considers Shepard a mentor even if they denie her access to infomation about the geth that would have allowed her to complete her Pilgrimage in the first game. Stockholm Syndrome applies to aliens.
Villainous Breakdown: Harbinger, who is normally unflappable, really starts to make it clear how much trouble Shepard is at the end of the Arrival DLC.
Harbinger:Shepard, you have become an...annoyance.
Violation of Common Sense: The SR-2 is boarded by the Collectors, who abduct the Cerberus crew. The only reason they succeed is because of the lack of any credible opposition as Shepard has taken every single one of their handpicked badass specialists (which can number up to 12 including DLC) and crammed them into the Kodiak (sardines, anyone?). Nor are you allowed to simply wait for however long it would take EDI to sync up the Reaper IFF. This is done to ratchet up the tension for the endgame, and give a sense of raised stakes, but getting to that point is pretty blatant railroading in a series that is normally much subtler about it.
In fairness, the reasoning is sound. EDI's testing theoretical technology, and it despite how bad it was that the rest of the crew was nearly harvested, the worst case scenario was the destruction of the ship and all aboard. It's possible, if expensive and undesirable, to replace Normandy and Shepard again, but it's unlikely that he could afford the time to replace all those dead specialists you spent the entire game recruiting.
Justified in that the squad is always deployed in the shuttle - that's why exiting a level allows you to either return to the Normandy or simply swap out your teammates.
Visual Pun: The M-300 Claymore is the most powerful per-shell shotgun in the game. Although its model number is M-300, the shotgun model has it printed as 300M. Because of the font, from a distance it can be easily read as BOOM.
Visual Novel: In-game, the Lair of the Shadow Broker DLC reveals that Legion owns the official game of Fleet and Flotilla (a film about a romance between a turian and a quarian), which, from all accounts, sounds like a Dating Sim. He really, really sucks at it.
Voice Changeling: It turns out that Morinth, by way of considerable practice, is able to do a perfect imitation of her mother, Samara.
The YMIR mechs tend to be difficult (especially two at once), but the Collector Praetorian on Horizon has heavy armor, flies, and shoots Eye Beams which can kill you in a few seconds. Just to make it even more fun, you have to keep your distance when fighting the Praetorian, as it slams down, releases a shockwave, and regenerates its barrier whenever you get too close. Thankfully, its armor doesn't regenerate along with it.
Horizon is one big series of Wakeup Call Bosses. First, you have Harbinger, which is doable. Then you meet your first Scion, an enemy which can pierce cover and requires you to do more than duck-into-cover-and-shoot. (Have fun dealing with that along with Harbinger as well!) Then you fight two Scions at the same time. Then... the Praetorian, who can kill you in the blink of an eye.
If you play it early in the game, the end of Kasumi's loyalty mission can count as this. Wave after wave of Eclipse troops and LOKI mechs, while a gunship is shooting its minigun and launching rockets at you... a gunship, mind you, that regenerates its shields after you take them down once. Oh, and did I mention that Kasumi is your only squadmate in this fight?
Walk It Off: You now auto-regenerate health, to help take the game in a more shooting-oriented direction. This was possible in the first game, provided you met certain conditions, but it wasn't a viable mid-combat strategy.
You can also walk off your tipsy drunkenness after a couple of seconds, which may be explained by Shepard's cybernetics filtering out toxins more efficiently than a "standard-issue" endocrine system, as evidenced by a dose of poison in a minor sidequest that should kill a normal person, but merely knocks Shepard out for a bit.
War Memorial: In one of the DL Cs, Shepard can erect a memorial to the fallen crew of the original Normandy at her crash site.
The War Sequence: Tali's recruitment mission finishes with Shepard and co. fighting through an endless onslaught of geth, including a Colossus, in order to reach her.
Wave Motion Gun: The Thanix Hydronamic Cannon. It's a mass accelerator that fires jets of molten metal at near relativistic speed, reverse-engineered from Reaper technology. You see Sovereign wielding the originals and skewering many Citadel ships with it during the Battle of the Citadel.
Weakened by the Light: This happens to you, during Tali's recruitment mission, which takes place on an old abandoned colony orbiting a star that is, for unknown reasons, aging rapidly and putting out too much radiation. Sunlight on this level burns out the shields of you and your party members, so you need to duck into cover and shade to allow your shields to recharge. It doesn't do any damage to your health, but without shields, you die from gunfire very quickly. Averted by the geth, in said mission. Grunt also averts it, because he never uses shields anyway.
Weaksauce Weakness: Husks. Creepy, they come out of nowhere and they charge right at you with that disturbing wail. And if you send them flying with biotics or Concussive Shot, they instantly die.
The geth pull this off, too, with implications that messing with them on any level is a bad idea, even after their defeat. Explained by Legion, who points out that the geth do not consider themselves robots, but programs. Any access to their data is likely to free them to corrupt or subvert other systems.
The realization during a sidequest that the Collectors are genetically altered Protheans after getting a clearer look at the recurrent vision from the first game.
The moment when the Normandy is boarded by the Collectors, who get away with everyone except for Joker and the crew.
The Arrival DLC. Not only are the Reapers incredibly close to the galaxy, but Shepard is forced to kill 300,000 batarian colonists to destroy the Reapers' shortcut throughout the galaxy. There is no big moral choice. There is no choice, period. And it's only a delaying tactic.
Harbinger's manifestations. Especially when realizing how similar it is to the Rachni Queen's possession techniques in the previous game.
Kaidan/Ashley gets one when Shepard shows up on Horizon.
Players can give one to Liara when you find out she gave your body to Cerberus.
And before that Shepard can say (for some weird reason the line gives you Renegade points):
Shepard: You're threatening to flay people alive now?
In the Arrival DLC, you get a huge one from Admiral Hackett after blowing up an entire system to delay the Reaper's invasion...and killing 300,000 batarians in the process. Toned-down slightly in that he says he knows you had good reason to do so and he'll offer to do everything he can to hold off the Alliance pressing charges, but warns you that your actions may lead to all-out war between the humans and batarians, and that Shepard will eventually have to face the Alliance in a court of law.
If the player speaks to him after the Collectors abduct the crew, Joker will give Shepard an absolutely blistering one (and rightfully so) for taking every specialist along in the shuttle, leaving the Normandy essentially completely defenseless.
All of this can be subverted or played straight like mad, depending upon whether Shepard destroys the Collector base or hands it to Cerberus.
Tali will give Shepard a heartbreaking one if they chooses to reveal the evidence discovered on board the Alarei to the quarian Admiralty Board and Migrant Fleet at the end of her loyalty mission.
Doctor Chakwas briefly chews you out for not arriving sooner and not being able to save Kelly and the others if you take too long to go through the Omega-4 Relay.
And accidentally Tali's father. Suddenly exile becomes a preferable option for her.
Heavy implications of this surround the Illusive Man, who only breaks character in the epilogue of the Paragon ending. Prior to that, he claims that he respects Shepard's goals and motivations regardless of disagreements, but destroying the Collector Base shows Shepard or Joker his true colors.
The point of Legion's loyalty mission. You can either brainwash the geth heretics or destroy the handful before you. Only the immediate squad and the Illusive Man will ever know whether you decided to mind control the geth — you know, like the Reapers do to their victims — or willfully risked further genocide. Neither of them are really portrayed as morally right or wrong.
This is part of what drives Garrus during his loyalty mission. Only he and Sidonis know about the latter's betrayal of Garrus's squad, so he feels that he is the only one capable of delivering justice.
The conclusion of Samara's loyalty mission. Should you succeed in resisting Morinth's Mind Control (with sufficient Paragon/Renegade points), you can choose whom you want to take with you. If you decide to choose Morinth, she will kill Samara and assume her place on your squad. With enough skill that she can imitate her mother's looks, actions and speech, her true identity will remain unknown to everyone except the both of you. Not the mother of her latest victim, nor the Illusive Man or any of your squadmates (except for Kasumi, who will warn you about her after the Suicide Mission), not even the Shadow Broker will know.
At the end of Miranda's loyalty mission, she prefers that Oriana not know the lengths she has gone to keep her sister away from their father's influence, much less that she even exists. It's up to Shepard to get her to introduce herself to her sister.
Shepard: She doesn't need any details, but would it really be so bad for her to know she has a sister who loves her?
When You Coming Home, Dad?: The relationship between Thane and his son. The achievement for his loyalty mission is called "Cat's in the Cradle."
As for less sympathetic fathers, see the trope above this one.
Wicked Cultured: Donovan Hock, the antagonist of the Kasumi - Stolen Memory DLC. He even has (what's left of) Michelangelo's David and the Statue of Liberty in his vault. Naturally, Kasumi is jealous.
With a Renegade interrupt, you can destroy one of his prized pieces, forcing him into a less tactical approach.
Illium, which is as dangerous as Omega but subtler about it. Garrus will describe the many ways one can mess up and regret it on Illium, while Tela Vasir from the Lair of the Shadow Broker DLC says, "Illium is just like Omega, only with more expensive shoes."
Bekenstein, from "Kasumi - Stolen Memory" DLC. It's described as a human-exclusive Illium.
You Bastard: If you choose not to save the factory workers during Zaeed's loyalty mission, you have to listen to them scream as they horribly burn to death for most of the rest of the level.
BioWare furthered this with an update that made mining a little faster, then the Lair of the Shadow Broker gave you the ability to earn materials by sending agents on missions, as well being able to buy info on/mine planets with an abundance of a certain material.
You Shall Not Pass: Done in the Suicide Mission when all but two squadmates and Shepard stay behind to keep the Collectors at bay and give Shepard a chance to destroy the base. Depending on your choices, any or all of them might not make it. Before that, when the Collectors board the Normandy, the crew engages in a valiant holding action, with nothing but pistols and assault rifles, to buy Joker the time he needs to quickly limp to the AI core.