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There's also the descriptions of Brittney getting buried alive in Hunger. It'll make you claustrophobic on the spot.
Interestingly enough, the scariest part of book 1 was descriptions of Mary purging. It was just so graphic and realistic.
Drake beating Sam almost completely to death with his Combat Tentacles in Hunger.
There's no specific moment, but the descriptions of anyone that the GaiaphageMind Rapes are pretty scary. A particular shout-out goes to Lana and her Heroic BSOD.
Poor, poor Diana in FEAR had to give birth in a hot, dark mine.
And she was being slave-driven by Drake, Brittney and Penny before hand. Just before she goes into a agonizing and undignified labor, Penny makes her believe that her baby is bursting out of her stomach...And that it's a giant bug with Caine's face which is eating her. According to Penny, she didn't just see it, she truly felt it.
After she gives birth, Penny makes her believe she is pregnant with 1000 rats which chew through her womb.
Dekka is half eaten alive by bugs which burst from her stomach...She is then fully-conscious as Sam literally burns her flesh to kill the bugs, with Lana healing her horrific injuries so she can't pass out/die. She actually begs Sam to kill her.
Mary and Francis's fate in FEAR...They are so horribly deformed that the people who found them thought they were road-kill.
The descriptions of Astrid biting off Drake's nose and gouging out his eyes is pretty graphic in LIGHT.
In Light, every scene with Gaia, who possessed Diana's baby girl, using her powers to murder helpless children, and killing Brianna.
The adult's reactions to the kids in "Light" always terrified this troper.
To clarify, they see the way the kids have been living and just what has been going on, and they're horrified. Many of them are initially calling for every kid in the FAYZ to be killed, thinking that they're all evil and beyond saving.
Most of Drake's dialogue towards Astrid. He's talking about killing her (which is scary enough considering it's Drake) but it sounds like he's planning something else...