A scene in "Looking Glass" features Ray drugging Marcus while a person nearby wearing a green morph suit dances erratically throughout the night, mirroring a similar scene in It's Always Sunny In Philadelphia.
One of the side missions involves the client mentioning "Johnny Five", including several of it's memes. Marcus picks up all references and even mentions the sequel, to which the client mentions 'we never speak of the sequel'.
One of the Driver SF clients is the former owner of a taxi company. He's bitter that apps like Driver SF have driven him out of business. Sounds unremarkable, right? It ends with an ambush by the Bratva. Might be a coincidence, but it's quite possible that the client was Roman Bellic.
During the Swelter Skelter bit, if Marcus talks to a guy shadow boxing, he'll get him to get even more pumped up, eventually making him say Valar Morghulis
Rarely, a person's profile will say that they're a descendant of Ned Wynert.
The folks in Gary's Games and Glory, the Hackerspace front business, comment about the stereotypically nerdy games they play. One of them plays a paladin of Arneson, another comments on a Collectible Card Game that bears a strong similarity to Magic: The Gathering, and yet another refers to paintingminiatures. The store itself has a similar name to Gary's Games and Hobbies, a real life game shop in Seattle, though this may he a coincidence.
Crocodile Hunter: Marcus, Wrench and Sitara have their opinions on this, about his death
Marcus:I've always wanted to swim with dolphins. No stingrays. Stingrays will be cool.
Wrench:Oh no, no fuck that Dude. Those fuckers killed the Crocodile Hunter.
Sitara:Good call on the stingrays. Those killed the Crocodile Hunter.
During the Haum Sweet Haum mission, the four patrolling bots are Inky, Blinky, Pinky, and Clyde - the names of the the ghosts in Pac-Man. The fact that they're roughly the same shape really hammers it home.
During Swelter Skelter, the Inception sound is lampooned by one festivalgoer who will apply it to anything you say.
The trophy/achievement for finishing the False Profits operation is called "Baby, I Got Your Money", referencing the song "Got Your Money" by Ol' Dirty Bastard.