Actor Allusion: The fic runs with these like crazy, from Sarah Walker to Junko Zayne Shepard to the Omar Smuggler Drebin. You might want to check in on the Characters page for the full set for major characters. Other ones on minor characters include:
Adam using a fridge as an Improvised Weapon in the first prologue could be a reference to the Memetic Mutation of Adam knocking out entire armies with common fridges and vending machines. He also later casually uses a public toilet's sink in the same way.
Garrus incapacitates a whole group of Drell mercenaries to get something the group needed, rather than negotiate it from the mercs. Jensen felt like chastising Garrus for it, but then he remembered that he would do the same thing+ Knocking someone out and stealing their important item is an accepted strategy in the source game.
In chapter 24, when trapped in a lab on board the Durendal, Adam's automatic response is to look for an air vent.
Throw It In: Conrad's "Shadowrun sourcebook" is actually Sarif's Hail Mary pass at preserving SI's cybernetics research. And Hein saw that the instant he saw it, and that's where he's getting all his new toys from. And IngusDei decided to add it in.
IgnusDei allowed Space Battles-based readers to vote on the characters who would follow Adam onto Noveria. In the chapters that followed, he included several asides that showed how the story could have been changed if different characters had been included in the party. He also held a vote on specialized equipment for the run on Europa Genomics.