If you look closely at one scene of the aforementioned introduction, you'll spot a Kyrati Rupee amongst the many currency symbols.
The entire trailer for Cyberdriver features a sentient car which is essentially a Distaff Counterpart to K.I.T.T.
Even better, the achievement for completing the final mission for that segment? Knight Ridden.
Lenni's video message to DedSec at the start of the "Hacker War" operation is an homage to Max Headroom, complete with wireframe backgrounds, jaunty camera angles and electronic stutters.
At one point, Marcus and Wrench have a heated discussion on who would win between Xenomorphs or Batman.
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'.
More directly he references Sergey Brin, the co-founder of Google. Both are of east European origin, preside over one of the largest technology corporations on the planet, and are avid yoga practitioners.
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.
One texting NPC's conversation Marcus can hack into is the opening lyrics to "Hello", an Adele song about trying to reconnect with one's ex. It doesn't go well for the texter.
The Shuffler sidequest with the audio logs is like if you crossed the Cthulhu mythos with the Blair Witch Project.
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.
Wrench wears a T-Shirt with the slogan "I am DedSec".
During the third mission in the "Moscow Gambit" DLC, where Marcus is destroying faux DedSec vehicles that the Bratva are planning to use for a Frame-Up, he can call out "The quarterback is toast!". Bonus points for that line also being spoken by a bespectacled Black and Nerdy hacker.