These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Accidental Innuendo: In a later level of the game (in which you revisit the Ishimura), there are ultraviolet floodlights set up to aid decontamination crews in scrubbing up bloodstains and such. Of course, most male gamers will read something different into white stains under black lights. (The fact that they are huge just makes it that much funnier.)
Anticlimax Boss: The Tormentor has an awesome design; it's unfortunate that the "fight" against it is more or less a quick-time event.
Crosses the Line Twice: New Necromorph class the Pack, which are undead children. If Isaac is grappled by one and manages to shake it off, he'll punch the Pack's head off.
They managed to cross the line at least two more times in the sequel, now with a suicide bomber variant of the Lurker, the Crawler. Yes, folks: a dead baby actively tries to blow you up with an internal bomb. Its introduction? Isaac spying an obviously traumatized woman as he passes through the elementary school, that coo-cooes a crawler into her arms, and cradles it lovingly... which then goes kaboom.
Stalkers, which are just about the cheapest enemies you'll ever find. They play hide-and-seek behind boxes (and there are always boxes), poking their head around corners just to see if you're still there. Then they charge at you with ridiculous speed, knock you down if you connect, then run away so fast that you need near-perfect reflexes to land a limb blow. Even if you do manage to blow away their legs, they get even cheaper. If you don't kill them quickly, they crawl at you (faster than most enemies can run) and swipe at you continuously until you die, which will be quickly. They also come in groups of 4 or 5, at least. Better have upgraded that stasis unit or better yet the force gun; you will need it.
Leapers (the two handed enemies with a spiked tail) were an annoyance in the first game, since their odd design makes getting a good limb hit in somewhat difficult but they weren't that quick or damaging. This game decided to rectify both those problems, turning Leapers into speedy little death-dealers that come out of nowhere. At least they're mercifully rarer than in the first game.
The Pukers, too, at least on higher difficulties. Probably the only Necros that dismemberment has no effect on (cutting the arms is pointless, and taking their head or legs off will only make them a little less dangerous), their vomit does a lot of damage, the vomit globs they shoot from a distance will slow you down a lot for at least 10 seconds, and when you cut the limbs off up close the puke goes everywhere and ends up splattering on you. Plus they do more damage than probably any other Necro, except maybe a Divider's head, when they grab you.
Game Breaker: The Contact Beam is impractical for use on a regular basis against standard enemies, so it's not a total gamebreaker. It is, however, a boss breaker. Brutes go down in two hits if you target their limbs, and even the final boss on hardcore mode is no match for the Contact Beam. The true game-breaker is the Hand Cannon that unlocks for beating Hardcore Mode, but by then, you've already beaten the game every way it can be beaten, so no harm there.
Goddamned Bats: The Pack, depending on your surroundings. They're manageable most of the time, but there are occasions when you'll find them pouring out from several directions with no decent cover. Perhaps in acknowledgement of this, the final boss spawns endless waves of them to attack you (since she has a One-Hit KO attack and you need the ammo).
Nausea Fuel: The aforementioned Eye Scream sequence. It made a lot of players cringe whether they succeeded or failed. Urrrgh...
Paranoia Fuel: So, the Red Marker is finally destroyed...and the Titan Marker, too. How many are left? At least eleven.
There's one scene where you see a familiar hole in a wall, and hear a familiar wail. No giant tentacle bursts out to grab you this time, but it definitely brings back bad memories...
Lampshaded when Isaac hallucinates another repeat attack near the beginning of that level.
Special Effect Failure: The in-game engine is pretty bad when it comes to rendering objects at a distance. One glaring example is during Chapter 7 if you look down at the station, where it is obviously just a 2D image.
That One Boss: That freaking regenerating Ubermorph that you face off with at the finale. It's almost totally invincible and will hunt you throughout the level like a bloodhound. There is a way to kill it for good but it's tricky and completely optional due to the fact that it's a glitch.
That One Level: The decontamination chamber in the Ishimura returns. The chamber itself will let you off without incident the first time. The hallway past that more than makes up for it. It's perpetually dark. There are Pukers and Stalkers (the latter at least missing legs, thankfully) in addition to normal enemies. There are Elite Mooks that blend in with the darkness. Enemies just spawn out of nowhere, often behind you. It's cramped, which makes it that much easier for them to hit you. Did I mention that it's dark? Because I can't stress that enough. Then you go back to the chamber, which starts up again so you can be properly ambushed like last time.
The Woobie: Everyone with more than a few minutes of screentime has their moments. Isaac, Ellie, that guy that holds a knife to Isaac's neck in the beginning, hell even Stross before he goes really crazy and you're forced to kill him and even one right after that if you get the right audio tape.
He's not even really trying to kill Isaac or Ellie. He's just desperate for someone else to see what he's hallucinating so they'll be able to deal with it. The accusing stare of his dead wife is too much for him to handle; like Isaac says, in his mind, he's not attacking you, he's running from his own guilt.
Stross comes across like this. Yes, he's an asshole who goes insane and turns on you, but he motivated Isaac when he gave up hope and told him how to find and destroy the Marker (he was confused about the specifics, but he gave the right details), he is torn about his previous crimes, he obviously was never cut out for fighting these creatures, but he survives, and even Isaac pities the man and regrets having to kill him. Yeah, the background material makes him look worse, but some part of you HAS to pity the man for being in the wrong place at the wrong time. If the Necromorph's Markers hadn't driven him insane, it's easy to see him as capable of redeeming himself. It helps that all he talks about the whole game, even when insane, is finding and destroying the Marker. It's obvious he's trying to make up for failing to destroy the last one he came across due to fear.