The original's "good" ending, in which you grow old with the Little Sisters you saved, and you finally have the one thing you were denied: a family.
Thanks to Bioshock Infinite, this is the canon ending now.
Saving each Little Sister is a minor CMOH in itself: you put a gentle hand to the girl's brow and hear her gasp/sigh, along with a few bars of Garry Schyman's achingly sweet violin theme, as everything goes white. When you can see again, she thanks you and scampers off to the nearest vent.
BioShock 2's ending, in which Delta lives on through Eleanor.
In BioShock 2, sparing Grace Holloway's life, and seeing her amazement after you leave.
Grace: You had me under a gun... and yet you just walk away? No monster alive turns the other cheek. No monster does that. A thinking man does that.
In BioShock 2, there's a diary who is owned by a little boy named Billy Parsan. In it, he tells a Little Sister that he thinks she's cute, her Big Daddy reminds him of a Comic Book hero, that he bought her a gift and stored it someplace that no one else could get it, and said he'll wave to her next time he sees her. I guarantee you will go "D'awwww!"
Even more so when you go to where he says he left the gift: It's a rose. Heart: Broken.
Which then becomes a Tear Jerker when you find it by the corpse of a Big Daddy that was most likely her protector seeming to have been bringing it to her.
Heck, there was a Crowning Moment in the very first trailer ever shown for the game. We get a savage battle between a Big Daddy and the player who was trying to take a Little Sister. It ends with the player getting gored to death by the Big Daddy's drill. As a camera cuts to the Little Sister cowering on the ground, the Big Daddy stomps into view towering over her, his drill still covered in blood, and reaches out his huge hand to help her up. That single shot let me know that this game would be different.
Big Daddies in general draw an inexplicably perfect balance between terrifying and CMOH.
Even playing as Delta gives you the feeling of being a sort of Frankenstein's monster.
Near near the end of the game you can see the world through the eyes of a Little Sister and one of the first things you see is a two story high golden statue◊ of a Big Daddy in a heroic vein looking something like a knight Templar or a paladin. Also all of the other statues you pass during the mission are of Big Daddies being heroic- protecting people and defeating monsters. It's nice to know you're a hero to someone after all.
The very FIRST thing you see is Delta, pimped out in gold and white◊ and looking like a comic book superhero. The statues previously mentioned are of Delta's actions throughout the game ("Daddy Meets Aunt Gracie", "Daddy Meets Uncle Stanley◊", "Daddy Meets Dr. Gilbert"). Of course, even if the player had killed the people depicted, the statues portray the kills as more of a "righteous fury" type of thing (you ARE looking through the eyes of a Little Sister, after all). The entire mission also doubles as a scary moment for some.
There is a moment in Fontaine Futuristics when Sinclair says that he feels sorry for Big Daddies. It was good to know that the current Atlas-analogue was a good person who could empathize.
Even better, Lamb constantly tells you how shifty Sinclair is and how he's only interested in profit. But he never betrays you, suggests the "good" option in several cases, and even tells you how there is a way to make you human again. In the end, all he wants is to do something good after all the bad he did in the past. Not only that, but he actually proves Lamb wrong.
Thus Sinclair is the antithesis of Frank Fontaine, and in many ways the real Atlas compared to the fake persona Fontaine created.
When Sinclair is turned into a Big Daddy, he doesn't blame Delta for trying to kill him, and asks him to "Stick it to Lamb and let young Eleanor see the sun."
Minerva's Den. We FINALLY get a major character, C.M. Porter, who 1) Isn't a complete ass. 2) Was smart enough to see through Ryan, Fontaine, Atlas, AND Lamb. 3) Resists one of the primal temptations and shuts down the AI construct he made of his departed wife, knowing that it wasn't her or what she would wanted. At the end we see this poor man's grief, and how he refused to let it break him or twist him like so many others in Rapture. And the best part is that HE LIVES!
He's also similar in some ways to Bill McDonaugh. He was loyal to the ideal of what Rapture could have become yet never lost his humanity in the process until becoming Subject Sigma and never really spliced himself up or let himself get swayed into the madness like so many others. He was by most accounts one of the nicest people in Rapture, even during his worst moments; in fact (similarly to Bill and his family) he loved his wife so much that he wouldn't let himself recreate her via the Thinker. If anything, he's vindicated what Bill stood for.
If you've been saving the Little Sisters throughout the first game, you'll see all of them playing in Tenenbaum's sanctuary. They basically start heaping praises onto you and say you're going to save them. That fact alone can give you the fuzzies.
In BioShock 2, when you get the Hypnotize plasmid, you see a pair of splicers slow-dancing, acting completely enamoured. It was obvious that you were supposed to use the plasmid to turn them against one another, but it brought back fond memories of this troper's home-coming semi-formal. He just couldn't bring himself to harm either of them, and left the area without killing either of them. It was the sweetest thing he'd seen in Rapture for a long time...
One of them had even brought a gift!
Fridge Brilliance / Horror - after what Lamb did to you with the very same plasmid, years ago, you'd have to be as much a monster as she is to inflict the same on another. "So," the game asks, "are you?"
In the early parts of BioShock 2, it's possible to find the audio diaries of an industrialist by the name of Prentice Mill: he apparently founded and owned the Atlantic Express railway, and from what can be heard of him, he was also something of an arrogant jackass. However, private bathysphere travel made his railway obsolete, and the bank crash that followed the New Year's Eve Riots left him completely destitute: his last audio diary mournfully notes that he has no family, no friends, and nobody likely to miss him. So, why is this not a Tear Jerker? Well, you find this last audio diary on a small shrine in Pauper's Drop, one built specifically for him. It's not known if he only stayed in the Drop long enough to kill himself, or if he made some kind of life for himself; all that's known is that someone cared enough to leave a memorial to him.
This one is ridiculously minor, but it's still pretty striking. In the first game, there's a Splicer model and voice pack called Toasty, who's deluded himself into thinking he's The Casanova, making flirty comments half the time, but switching to misogynistic comments as well when he realises the flirting doesn't really work. In the second game, that Splicer model comes back, but with changed lines. All the angry comments are dropped, and most of the flirty ones are too. Why? Because, whether it's real or just in his head, he says he's gonna be a dad! Even in the watery hellhole that is Rapture, he's just worrying about the nursery room and his wife. True or not, it's amazing to hear someone so excited about something so normal. Of course, this may cross over into Tearjerker too...
Depending on your actions, when you are temporarily a Little Sister the statues you encounter on the way can be either this or nightmare fuel: one of the statues, the one representing how you treated Stanley Poole either shows you killing him or helping him stand on his own two feet again. The one representing Gilbert Alexander is perhaps the most impressive: if you did the right thing, it shows Delta pulling a man out of a monster.◊
Near the end of Bioshock 2, there's a big one for players who have been good. Big Daddies have yellow portholes as a default, red when they're attacking, and green when they're hypnotized. Big Sisters have red. Always. Until, looking through the eyes of a Little Sister you're possessing, you see Eleanor Lamb towering over you with a green porthole, as she reaches down to release the Little Sister from her slug, while talking about how you've taught her to be good.
The Thinker is an advanced A.I. who isn't sinister or out to Kill All Humans. Instead it impersonates its creator, who was turned into a Big Daddy, in order to save him and help him to regain his old memories.
Doubling with Tear Jerker: when you're exploring the amusement park in the second game, you find a series of audio diaries from a teacher who was trapped in the park with her students when Rapture's civil war started. She ends up dying of starvation because she gave all her food to the children. Where do you find her body? In a high-up corner where the Splicers can't get her, laid out on a rug with arms folded over her chest, surrounded by candles, gifts, and drawings of smiling children. The children knew what she'd done for them, and they honored her as best they could.
In Bioshock 2, if you take a moment to watch the Little Sisters while they are with other Big Daddies, you may see that sometimes one of them may stop and sulk while refusing to move forward. The attending Big Daddy will gesticulate with his hands and grunt gently at his ward as if to say "Come on, just a little more" before gently patting her head. The Little Sister will look up at him and continue onward.