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.
Complete Monster: Genevieve Aristide is responsible for the events of the first game, opening up the vault despite the head of that project telling her what a horrible idea it was. When Alma's mental ghost manages to break Paxton Fettel out, her main priority is to cover up Armacham's involvement in the whole affair, ordering their security teams to kill one of her own employees who knew too much. In the second game, it's discovered she also authorized two more unethical Projects; Harbinger which tried to take sick individuals and transform them into another Psychic Commander, but only survived to twist them into monstrous forms. The other was Project: Paragon, which involved taking children with promising mental and physical attributes and enrolling them in a fake elementary school, where they would be fed chemicals to grant them psychic powers and sedatives so they could be taken to an underground lab, all in the hopes of finding future candidates for Harbinger. And when all of these projects blow up in her face and result in the city being devastated by a massive explosion and Alma's psychic outbursts, her main priority is capturing Alma so she can maintain her position in Armacham, sacrificing Beckett to be raped by Alma and killing Stokes to prevent her from interfering.
Contested Sequel: Every F.E.A.R. game and expansion since the first has resulted in reams of discussion as to whether or not it matches up to the original.
"Funny Aneurysm" Moment: Stokes asks Snake Fist who Alma is. Snake Fist replies "She's the mother of the apocalypse!", an amusingly unhelpful description that becomes somewhat less amusing in light of the game's ending.
Especially considering you are the father of the apocalypse.
Hell Is That Noise: Some of the automatic doors in the second expansion pack seem to be designed to produce the a sound that is painfully close to the same sort of laugh as the near invisible creepy monsters which show up in both of the first game's expansion packs.
Hilarious in Hindsight: One of the meanings players gave F.E.A.R. was "Fuck Everything And Run". In FEAR 3, one of the multiplayer modes involves doing mostly this and is called "F**king Run".
It Was His Sled: F.3.A.R. is built off the twist endings of both games prior: Paxton Fettel being the Point Man's brother and Alma being their mother, and Alma raping Beckett.
Moral Event Horizon: Genevieve Aristide and Harlan Wade. Which of these two is worse is up to you, though consider Alma's forced impregnation, the sperm donor of which is her father. The bastard basically knocked up his own daughter.
Paxton Fettel crosses this if you win F.3.A.R.'s campaign as Fettel. For someone obsessed with talking about his mother with his brother, it's horrifying to see Fettel absorbing Point Man's body to eat his mother. It's easy to lose any sympathy for him after seeing this ending.
Narm: The aforementioned "free pizza at an anime convention" line, though it may have been deliberate on the part of the writers.
Paranoia Fuel: Alma is standing right behind you. ..... Made you look.
Oh look, there goes any sleep I might have been getting for the next week. Yep, right out the door, and it's taking the car with it.
This is brought in full with Jankowski's ghost; at various points across the game (and some of the expansions), you'll hear his voice echo, "Is someone there?".
There's a scene in F.E.A.R. where you get out of an elevator, walk maybe 10 feet away, and press a button or two to get the elevator working again. Then you look up and Alma is standing there, between you and said elevator.
There's an Assassin in the room with you. Don't worry. He's just going to follow you everywhere and keep telling his friends where you are at all times.
That One Boss: In F.E.A.R. 3, the REV powered armor in Interval 05 that appears in the plaza. Most such units in previous games were weaker, to the point that all it took was a few assault rifle magazines to destroy. This one eats bullets and explosives and laughs, and then returns the favor with lasers and automatic grenades.
Uncanny Valley: One review of the first game noted that, while the graphics were impressive, the characters more closely resembled plastic dolls than real people.
ATC troops in the first and second games do not change their facial expressions, even when getting shot or torn to pieces by psychic horrors. This may be why the ATC troops in the third game were all rendered with balaclavas to hide their faces.
The Woobie: You can't learn about Alma's background without feeling somewhat sorry for the girl.
And let's face it, Becket at the end of F.E.A.R. 2. He's been fighting for two days straight, got horrifically operated on, is having horrible hallucinations, is being attacked by endless numbers of enemies for no discernible reason, is stalked by an insane psychic ghost, gets raped and becomes the "father" of the apocalypse. It gets worse for him in F.E.A.R. 3, as he's escaped only to be captured and held by Armacham for nine months, then gets his mind invaded by Fettel before exploding. And worst of all, no one let him change his clothes in nine months. Poor guy.
Then there are the Replicas, if you think about it too much. Do they actually want to be shooting at you, or are they just being forced to do so by Fettel? And, then there's Fettel himself, who is being driven insane by Alma.