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.
Anvilicious: Daemon is somewhat subtle in pointing out an actual evil. Freedom™... less so.
Complete Monster: The Major brutally kills Roy Merritt, cuts off/out Loki's fingers, tongue, and eyes, orders his mooks to throw Sebeck and Laney into a wood-chipper, and saves teenage girls from brothels... so that he can get them Darknet accounts and then behead them to steal their Darknet identity, keeping their heads chemically alive to spoof the biometrics. Oh, and he came up with the real "Operation Exorcist" plan to expunge Daemon from civilization: Alpha Strikes. Invade Darknet communities with full military force, then send in mercenaries who proceed to destroy every piece of technology present and execute every man, woman and child.
Fridge Brilliance/Fridge Logic: On one hand, everything worked perfectly. There were no bugs, glitches, mistakes, etc, despite the fact that there couldn't have been real world testing, beta testing, etc. The Daemon responded properly every time, and all the schematics produced working devices. On the other hand, Sobol was a genius with a ridiculously high IQ of 220. You can probably infer he was among the smartest people to have ever lived. Maybe he was just that good, putting this into Fridge Brilliance.
Sobol only had to predict how officials would react well enough to give time to get human operatives into the network for resilience. He probably didn't have to guess real hard.. And after all, his goal in the end was to get enough humans into the network that they could sustain themselves without his help. The daemon itself was ultimately just an effective Trojan into human society.
Jerkass Woobie: In Freedom™, Loki graduates to this from a regular Jerkass when the Major captures and tortures him, chopping off the tip of each finger, cutting out his eyes and his tongue. He briefly returns to being a Jerkass after being saved by his Nazi buddy, but hurriedly returns to Woobie status when the Burning Man bot cuts him down to level 10, stripping him of the power he had worked for years to obtain (and been tortured for). Even the other members of the Darknet agree, gathering around him as he cries.
Nightmare Fuel: The fact that the Daemon is not self-aware or intelligent is brought up a number of times with certain characters who realize that once it has them in its power, there is nothing they can do to argue or reason with it. They are told that any deviation from the script will trigger the "you die" action. Based on the answers they give to the script, they may die anyway.
The AutoM8s. Murderous, autonomous, armored, solid-tired Humvees that are essentially invulnerable to anything but anti-tank weapons. And completely possible to build in reality.* Good luck programming the damn thing, though!
The Razorbacks. * shudder* They are intentionally designed to inspire terror, especially once you've seem them in action. Jet black, armored, autonomous racing bikes covered in shark-fin-like metal blades and shamanic runes and symbols, 3-foot long blades mounted on articulated servos instead of handlebars and blinding lasers to incapacitate you. They can operate in close-quarters (i.e. inside buildings), their hardened blades are sharp and fast enough to cut a man to pieces and then cut the pieces to pieces before they hit the ground. There is no attempt to stealth them, so you can hear them coming. And Loki has a semi trailer full of them.
Well, no attempt to stealth them... unless they're running on the internal flywheel drive, which can sustain them in complete silence and darkness for a few minutes. Good luck guarding that base, unfortunate mercenary.
Spiritual Licensee: Watch_Dogs is essentially the Daemon's Darknet for PS4, and Aiden Pearce is essentially Matthew Sobol minus the terminal cancer that forced him to empower Brian Gragg AKA Loki Stormbringer as his successor in his war against corruption.
Tear Jerker: The Major decides Merritt must be liquidated and shoots him in the back from a helicopter during the final, epic chase between Merritt and Gragg. As Merritt is lying on the ground, waiting for the final shot, he struggles to get the two photos of his daughters that he always carries with him. They are the last things he sees before The Major blows his head off. Even Gragg is horrified.