Chapter 3: "Look, You want to run this job?" "Actually, yes, I do want to run this job!" "Well guess what? You CAN'T. Now get behind cover and keep your mouth SHUT. Your constant yapping is harming my calm."
Chapter 4: "You were dead, Mister Vakarian..." said the human as he unhooked the cardio-stimulators from Garrus' flesh. "Too soon, too soon! Fist wants you to suffer at least two days, minimum!"
The salarian in that scene is also wearing Jayne's "cunning hat."
If you didn't pick up on it, the human is Niska.
Chapter 7: "Someone tries to kill you, you kill them right back!"
"They'll beat us, hang us, then burn our corpses, and if we're lucky, they'll do it In That Order."
Chapter 9: There was a Sergeant Reynolds involved in the defence of Elysium.
Chapter 15: Garrus rolled his eyes. "A shapeshi- oh come on, Jensen! Sounds like something out of a bad sci-phi!" "...You live on a space station." "...Yeah, so?"
Chapter 22: The 23-G Bellum Compound turns people into Reavers with shorter life-spans.
A salarian named Mister Weltall(German for Universe) took footage of Jensen's skycar chase.
'For years to come the Triumvirate would try to explain to themselves — through science or faith — exactly what had happened, but suffice to say that a monster had been loosed, and that it wanted its maker dead.'
The director of the Subject Zero project was surnamed Aristide.
The slavers in chapter 20 took an Omar called Drebin.
Stabbing a guy with a blade embedded into your foot.
Adam pulls "a cord with glowing blue power cells plugged into it like bulbs of garlic on a string" out of a Geth.note The stuff you get for doing Zandatsus in Metal Gear Rising: Revengeance. He does a similar thing to finish off Benezia.
"I heard he was as strong as a titan and lifted that damned Red Wanzer and threw it into the sun!"
"Nanomachines, son. ... How did this guy survive a gunshot wound to the head? Nanomachines. How come those missiles exploded spontaneously? Nanomachines. How did that crazy fucker regrow his head and arm? Nanomachines, nanomachines, nanomachines."
Five of the bullets Sandal gives Adam in chapter 38 correspond to some of the elements from Damage 2.0: Blast, Electric, Corrosive/Toxin, Cryo, Magnetic.
Ramsus uses a "Nyx" hardsuit and pulls off Absorb at the end of chapter 40.
In chapter 41 Adam sees Promethean tablets containing Oxium.
A monster called Lephantis appears.
The Gaians were Precursors who could turn technology against their users.
Corrupted enemies controlled by devices on their heads appear in Interlude 3.
In that same interlude, when Subject Zero goes berserk, she is surrounded by red energy and is using "biotic claws" to tear apart everything in her path... which is pretty much exactly what Valkyr's "Hysteria" power looks like.
A hooded guy sitting on a bench trying to stay inconspicuous.
In chapter 41 Adam's melee fighting styles is compared to ancient assassins wielding dual arm blades.
An actual Hidden Blade shows up in Interlude Three, and is equipped by a Templar named Kenway. There's also multiple other references to the Assassins, and one of the Templars thanks the "Father of Understanding".