In the mission shown during the gameplay demo shown at E3 2012, Aiden is shown killing Joseph Demarco. The mission was changed prior to release, and instead killing Demarco, Spoiler:Aiden now has to kill a hacker, Defalt.
The town Pawnee is based on the real life town of the same name. However, the game portrays Pawnee as being located right outside of Chicago, when it is actually located near central Illinois.
While modding the PC version, a user by the name of "The Worse" found almost all of the shaders and graphical improvements present in the 2012 and 2013 trailers for the game. It's possible that the PC version's graphics were downgraded so that it would not make the PlayStation 4 and Xbox One versions look drastically inferior by comparison.
In some randomly generated vehicles, there is a chance that the keys will have a keychain of what appears to be a My Little Pony character dressed as Aiden.
Inside Iraq's hideout are a number of arcade machines featuring the logo of Far Cry 3: Blood Dragon.
During one of the optional Privacy Invasions, the player can see an emotional discussion between a stage II cancer patient and a woman working two jobs. The conversation and characters themselves are a direct reference to the TV series Breaking Bad.
Graffiti can be found around the city that resembles the Slenderman.
Aisha Tyler (famous for her role of Lana Kane in the animated comedy Archer) makes a cameo appearance as herself in the role of a citizen NPC. She can be discovered while exploring Chicago, but can be easily found in Connely Square just outside of the Willis Tower in the mission "A Wrench in the Works". She is also the subject of a Privacy Invasion activity.
Every sign in the game reveals a famous meme or quote when hacked.
Inside Nicole Pearce's house is a Rayman Raving Rabbid toy that laughs when hacked.
During one of the gameplay trailers. a man can be seen dancing in his apartment. His information states he is a video game store clerk and has legally changed his name to "Eddie Kenway". This suggests the man is a fan of Assassin's Creed IV: Black Flag, as Edward Kenway is the name of the main protagonist in that game.
One of the camera feeds that the player can hack into shows a father watching his son play a video game. The father is mocking how the assassin in the game talks to the people he kills. This is a reference to the Assassin's Creed series (also developed by Ubisoft), in which the protagonists talk to the people they kill before they die.
Watch Dogs actually takes place in the same universe as the Assassin's Creed series. This is proven by an email found in Assassin's Creed IV: Black Flag sent to Abstergo by Blume Corporation.