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!"
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.
The 108 was built by Shinkawa Heavy Industries. note Yoji Shinkawa is the main mechanical designer for the games.
Bioroids were hypothesised by a Dr. Drago Pettrovich Madnar.
Adam's daughter was named Sunny.
The slavers in chapter 20 took an Omar called Drebin.
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."
The Templar have a division called the Crimson Blades.
Others
In-Universe, Jenkins tries to use the fake name of Riddick. Adam plays along for a short while before pulling the rug from under him by telling Jenkins he's seen the Riddick Movies.
2050s university student MyronBoone invented Zyme.
There is a reference to "ghost-heads", psychotics addicted to being wrapped in a personal cloaking field, which points to both Fallout Nightkin and Homeworld Stealth Fighter pilots.
An operative Sarah Walker is assigned to the Normandy. For added fun, her namesake was played by Yvonne Strahovski, who's Miranda's VA.
Also, Wrex's contact with the Shadow Broker is "Agent Brea", another Strahovski role.
Jane is The Sneaky Guyof Native American descent who favors a tomahawk and knife. Only way it could have been more obvious was if her outfit was hooded and she used an Omniblade. In chapter 26 we learn that the Native American was her father and the Briton was her mother, who left her on the father's porch, as well as the father having been killed by a Kenway.
Also, Chad Dumier is a fan of the Tabletop Game, and has named the WTO's global exchange currency the Nuyen... which makes Conrad mistaking that sourcebook for a textbook somewhat more understandable.