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.
Anticlimax Boss: Mother Hydra. She has no way of actually attacking you, her only defense is a bunch of respawning Deep Ones, but they are absolutely no problem when the Yithian Lightning Gun can kill them in one hit and has infinite ammo.
Best Level Ever: One of the most praised levels in the game is the hotel escape, where you have to flee an entire town of cultists. You have no weapons, no allies, no mission... all you can do is run, bolting doors behind you while desperately trying to find a way out.
On the same token, the cutter level. To go into further detail: Jack has been fished out of the water by a Coast Guard Cutter (a ship operated by the coast guard that is at least over 65 feet long), when suddenly it comes under attack by the Deep Ones, who pour onto the deck and start killing everything. The crew arm themselves with Springfield rifles and Tommy guns, eventually fighting off the Deep One assault... then Father Dagon shows up. With almost everyone else on the ship dead, Jack singlehandedly takes down Dagon with the main gun by firing missiles into his face before Dagon manages to sink the boat. Unless you get the Game-Breaking Bug in which the ship doesn't get close enough to shore for you to target correctly, resulting in a game that can't progress.
Breather Level: The surface of the Devil's Reef. The level is quite short, devoided of enemies, and miss sanity-damaging stuff.
Crowning Moment of Awesome: By the end of the game, Jack has done several awesome things within the week. Namely, he fought his way out of Innsmouth, killed a number of cultists, destroyed a shoggoth with factory machinery, blew up Dagon by blasting him in the face, vanquished the cult leader Robert Marsh armed only with a knife, took on two Flying Polyps on very unforgiving terrain, dismantled the Esoteric Order of Dagon and electrocuted Hydra. All without going completely insane. Until the ending, that is.
Disappointing Last Level: A pretty serious case too, it's quite clear that most of the game's development went into the first half of the game. The last two levels are particularly problematic.
Fridge Brilliance: Jack's ability to take over the body of a Deep One seems out-of-context at first, since up to that point his Psychic Powers only went as far as a few random visions. However, it makes a lot more sense when you realize that it's an inherited Yithian trait, the ability to swap bodies across space and time.
Most Annoying Sound: "Spread out! Search the area!", which is repeated over and over and over again by the Innsmouth residents.
Narm: The slow motion effect that kicks in upon a Game Over also slows down dialogue. This is mainly noticeable on the rare Non-Standard Game Over where Jack is still alive to say something, like failing to save Hoover
Also the scene where an FBI agent has been covered in Shoggoth acid and can only yell gibberish as Hoover tries to get him to say what he ran into. Eventually, Hoover takes out a gun and shoots him. He then turns to you and says: "What're you looking at me like that for? He was an agent, he knew the risks!"
And about the shoggoth itself. It's gigantic, capable of forming eyes, mouths, tentacles and weird "blossom"-things wherever it wants to attack you. One thing that was added to the shoggoth for this game that makes it even worse is that its entire body is highly corrosive and will hurt you just by brushing up against it. Oh, and staring too long at it makes Jack (justifiably) freak out so much his vision blurs and he mutters to himself in a panic very rapidly. If not for the fact that it's sitting in the middle of a bunch of dangerous industrial machinery you would be totally unable to hurt it.
In the Innsmouth jail, the only other inmate besides Burnham is an insane lunatic named Henry rambling about, among other things, the rats in the walls. When you go through the sewers to get into the garage, you can find long-dead rat corpses and take one to show Henry that the rats are dead. Henry promptly devours the rat and kills himself by repeatedly bashing in his head against the jail bars, splattering blood on you.
Porting Disaster: The speed of every character is decreased in the PC version compared to the Xbox version. It makes the game nearly unwinnable when the last level ends with a desperate run toward a gate while the ceiling is collapsing. The Steam version lacks this glitch, though.
Squick: Mother Hydra. She has scales, is grotesquely fat, has razor sharp teeth, and has four giant breasts. She's just... gross.
That One Boss: The pair of Flying Polyps. Though they don't do a lot of damage to you when the attack, the terrain they are on is narrow enough to fall off if you walk carelessly. Add in that their method of attacking involves pushing you our pulling you towards them with powerful winds makes this even harder.
In addition, you have to fully charge your Yithian weapon (which is the only thing that can hurt them) and fire at them. Oh, and they can teleport.
That One Level: The penultimate level in the Deep One's underground city is absolutely infuriating in just how annoying it is. Mostly because it has one of the most insane, long, and Guide Dang It puzzles in the history of video games that requires a bunch of backtracking and searching.
What an Idiot: Robert Marsh has Jack at his mercy towards the end of the game. So what does he do? Instead of killing him, he throws him into a brig. With a chisel inside.