In Derelict Row, you can find a graffiti picture of the Dopefish, an enemy originating in the Commander Keen series of games by going through the sewers.

In the sewers of Lower Hengsha, there is a breakable wall only accessible with the Punch Through Wall augment. Inside the room are several Nuke Virus Softwares, a Valve to turn off poisonous gas, and two dildos on a mattress next to a bottle of lube and box of tissues.

The two dildos caused the game to be delayed in Japan for about a month, as it was slated to be released in September 2011, but was delayed until October 2011, as the Japanese ratings board prohibits the depiction of sex objects in retail games. According to Matthew Kowalewski of the Super Best Friends Play youtube channel, who worked as a QA Tester at the time for Square Enix's Eidos Montreal, they had to go as far as to do "Dildo Duty", which involved manually searching the China levels for any potential remaining dildos that may have been left over.

In the Director's Cut version of the game, they are completely absent from the game for all regions.

In the Hengsha Court Gardens, there's a bathroom with three seashells rather than toilet paper.
This is a reference to a scene in the 1993 movie Demolition Man, in which the protagonist discovers that in the future toilet paper has been replaced by three metallic seashells, though how they work is never explained.

During the game's opening segment in which the player and Megan walk through the facility, a man can be seen running on a treadmill for a set of tests. This was an homage to the 1970s TV show, "The Six Million Dollar Man", in which an astronaut had his body rebuilt with cybernetic implants after being severely injured in an accident.

The game's opening, in which the player walks through the labs while Megan talks to them and the various staff throughout the facility, was internally referred to as the "Walk and Talk", and was not included in the game's original draft. It was originally intended for the game's opening to be more like a training mission in which Jensen must infiltrate the company as part of a security test.

The developers originally wanted all news broadcasts seen throughout the game to feature fully animated 3D characters, but after some thought, realized that this wouldn't be possible with the scope of the game and the volume of content they would have to produce.

During the cut-scene that plays after the Tutorial mission at the start of the game, an Eidos Interactive logo can be seen on a building.

The Tranquilizer Rifle is called the "PAX-22". The word "pax" translates to "peace" in Latin. This fits with the purpose of the rifle, as it's supposed to be used as a peaceful solution for subduing enemies, rather than killing them.

Spoiler:If the player allows Faridah Malik to die, she can be found in the Harvesters' hideout on an operating table in the surgery. It's likely that she had been sold by Belltower to the Harvesters, allowing them to extract the augmentations that she mentions towards the start of the game that allow her to fly better.

The game's code still contains a number of debug menus. These menus include a map select that is available while having not started a game. This allows the player to start the game from any point in which they like - it also contains a number of unused areas, including versions of the game shown at press conferences.

While in a game, it's possible to access a menu called the "Burger Menu", giving access to general debugging options, as well as cheat options of spawning items, unlimited ammo, invisibility and immortality. The menu also reads a message in the corner that reads:

It is highly likely that the character of "Anonymous X" is a reference to the online hacker collective known as "Anonymous". This is reinforced through the cap that he wears, which reads "#Chan" - a reference to the collection of image boards, such as 4chan, largely considered the birthplace of the Anonymous group.

Arie van Bruggen, or "Windmill", has a large quantity of sticky notes plastered around the computer in his hidden room. These are reminders that he has left for himself, including reminders to call his mom and buy some broccoli and lube. On some notes, the ascii face "ಠ⁠_⁠ಠ" and the "Forever Alone" meme face appear.

If you go in to detective Murphy's office, you can catch him and another police officer talking about a 1980's Sci-Fi film where a guy "gets all shot up and gets rebuilt as a cyborg," which is similar to how Adam Jensen got his cybernetic enhancements. This and the detective's full name, Alex Murphy, is a reference to the 1987 movie Robocop.

Throughout the game are several "Final Fantasy XXVII" posters. This is a reference to Square Enix's Final Fantasy franchise.

The drop ship used to get around has the call letters "B-EE 008" on the side, but in the prerendered cutscenes (That were presumably made earlier in the game's development) the designation is "800 B-EE". It seems this was changed due to the fairly strong representation of the number 8 as a "B", meaning 800 B-EE would be pronounced "Boobie".