Whiling using the Cryptographic Sequencer, holding down all shoulder buttons while rotating the left analogue stick counter-clockwise and the right stick clockwise for around 5 seconds will make all characters have large heads. This works in both the standard game mode, and New Game+.

In the Industrial Area is a lone boat off the coast of the city. Using the Cryptographic Sequencer, it's possible to open a highly secured trap door into the body of the boat. Spoiler:Inside the boat are a number of The Scarecrow's experiments, namely cockroaches. There is also a thug sitting in a chair, who will scream when approached.

While fighting against The Joker, using Detective Mode's X-ray feature reveals that Joker has no bones. Spoiler:This actually foreshadows that he's really Clayface.

Using the Cryptographic Sequencer throughout the game, the player can find three hidden radio waves that transmit numbers.
These series of number can be deciphered with different mathematic methods, revealing a series of numbers, which need to be deciphered by correlating the numbers to letters of the alphabet.
Spoiler:These codes read out "I Will Return Batman", "You Will Pay For What You Have Done To Me", and "Fear Will Tear Gotham City To Shreds". The methods used to obtain these results, and their context, suggests that Scarecrow would return, which he would eventually do as the main antagonist of the 2015 game "Batman: Arkham Knight".

During the first mission, when fighting off thugs in the alleyway as Bruce Wayne, the player can see Azrael watching the battle on a rooftop to the right. He will eventually throw down a smoke pellet and escape.

Inside the room where the Riddler's third hostage is imprisoned, the player can find canisters containing Scarecrow's fear toxin, used for a Riddler challenge in Arkham Asylum.

Scattered all over Arkham City are newspaper clippings with the headline "Criminal Couple Gunned Down" and a smaller heading on the left that says "Boy Watches as Parents Die!". These are clear references to Prometheus, one of the famous villains in the DC universe, and a dark reflection of Batman.
Also, inside the old Gotham City Police Department building it's possible to find an Arkham Medical Examination Record for Prometheus, which states he "passed" and has been released on November 12th, 1982.

Inside the Gotham City Police Department building is a list of recently arrested people. The names are: Joshua Dahdrai, David Tyndale, David Higgins, Jigar Patel, Noel Chamberlain, and Johnny Armstrong.

All of these people are actually developers of Rocksteady Studios.

Playing the Joker's Carnival Challenge Map as Robin will have The Joker express surprise that Robin "is still alive." Joker is confusing this game's Robin, Tim Drake (the 3rd Robin) for Jason Todd, the 2nd Robin that Joker killed in the comics. Spoiler:Jason Todd appears in Batman: Arkham Knight as the eponymous antagonist, with a reference to Joker torturing, brainwashing and seemingly killing him, making it more odd he'd confuse Tim with Jason.

On top of a structure in the Industrial District near the Krank Co toy company building, the player can find Scarecrow's mask discarded on the ground. Scanning the mask is part of one of The Riddler's challenges.

In the Wonder City Foundations is a shop called "Toys & Dolls". On the door is a sign that says "Gentlemen's Hats & Accessories", and a picture very similar to the Gentleman's Ghost face, a character in the DC Universe. In the window is also a toy "Ghost Train".

It is possible (with a glitch) to get over the walls of Arkham City. Doing so reveals a completely modeled Gotham, Arkham Asylum, and other areas not visible from inside the city's walls. As none of it is solid though, it must be explored on a single glide.

Originally, Batman: Arkham Asylum was to be Mark Hamill's last performance as the Joker, as he wanted to leave on a 'high note'. However, after hearing that writer Paul Dini would return to write the sequel, and that Kevin Conroy would reprise his role as Batman, Hamill agreed to play the role one last time.

Spoiler:He would once more reprise the role for the hallucination scenes in Batman: Arkham Knight.

During Protocol 10, the player can find a patch of fire shaped like a musical note on one of the Museum exterior's side walls. It's unknown if this was a coincidence or a joke put in by the developers.

The Joker infects Batman with the TITAN disease by using his blood. This implies that the blood-type of Batman is AB+, or that The Joker's blood-type is O-. Either that, or they share the same blood-type.

This is implied by Batman not showing any signs of rejecting The Joker's blood. The Joker also has a plan to infect all of Gotham City with the TITAN disease by shipping his blood to the Blood Banks that supply the city. This would further imply that The Joker is actually a Universal Doner, otherwise everyone in Gotham with a non-matching blood type would die of Hyperacute Rejection.

At the end of Episode 3 of Catwoman's story in the Catwoman Bundle Pack, the player can choose to Spoiler:not save Batman, and leave Arkham city. The game will automatically rewind itself to the point before the choice was made. If this sequence is played backward, the Joker can be heard saying, "Thanks for the entertainment, Bats."

Early in the game, Batman must locate the source of a sniper shot. The Joker reveals that the church the gun is found in is filled with explosives, but the tower will not explode immediately if the timer hits zero. Instead, the Joker will talk for a short period, hinting at key plot points from later in the game.

After his monologue, the Joker will warn the player that they "really ought to get out of there." If they do not leave, the bombs will indeed explode, leading to a Game Over.

In the Steel Mill, looking on the floor in Joker's Office next to Harley's old outfit, it's possible to find a positive pregnancy test. Spoiler:This is an allusion to Harley's pregnancy in the "Harley's Revenge" DLC.

In said DLC, however, Spoiler:, this would become nothing more than a red herring, as when the player re-enters the late Joker's office, Batman finds a baby's crib containing the puppet Scarface painted to look like Joker. Surrounding the crib are a number of used pregnancy test strips, all showing a negative result. Inside the crib is another box the tests came in, with the box warning that the tests can sometimes result in false positives.

Throughout the city are a number of giant Cheshire Cat heads. There is also a giant yellow duck in the basement of the Steel Mill. These items may be in reference to Tim Burton's early Batman film, Batman Returns.

In "The Joker's Carnival" Challenge Map, reaching a 100 hit combo will cause the Joker to join the fight. He will have the same moves he has from the story mode and does not affect the score in the challenge.