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.
Nightmare Fuel: Dodge, whether he's in the guise of a normal person or a grotesque skull-reflection. Sam also counts. Lampshaded in this interview with Joe Hill, who stated that for him, the key to writing horror was "....to push the limits psychologically...to bring the heroes, and the reader, into an uneasy, uncomfortable place, and force them to live there a while." Seems to be working pretty well.
Tear Jerker: several moments, but something about Rufus telling his mom "I just want the commander to know if she's ever tired of me, the team will move out at her command. Say the word," i.e. that he'll leave her if he's a burden to her, just seems to have that extra sense of tragedy.
Never mind Rufus Seeing his mother's corpse after Dodge murders her. when the cop tries to hold him back, Rufus just whispers "let go of me" before kissing Ellie's forehead one last time.
So much in Clockworks. Poor Ben and Miranda Locke's backstory is sad enough, but even worse is finding out what a stand-up guy Dodge used to be.
Jordan selflessly giving up her life to save Jamal and Kinsey.
Scot using the last of his strength to help the survivors in the black cave get to safety, before finally using the Alpha key to kill the parasite in Jackie's soul so they could die together as themselves.
Scot: You all right, my love?
Jackie: Yes. Much better. You saved me. My hero.
Scot: All in a days work.
Pretty much all of Alpha #2. This troper sobbed through the whole thing.
Tyler finally getting to take a ride on Jordan's motorcycle.
The Woobie: Ellie Whedon, The Locke kids, Nina....