Edward Nigma / The Riddler
What's green and grey and covered with questions? Why, it's the next door down the hallway, leading to the cell of that King of Quizes and Master of Mindgames, Edward Nigma aka The Riddler. Unsurprisingly, the wall around Riddler's cell is decorated with green question mark graffiti and the riddle, "What is blue and grey and red all over?" (Best guess? It's either a dead Batman or The American Civil War.)
As a riot breaks out after Dr. Deegan opens all the cell doors to cover his escape, one inmate gleefully declares that the inmates are running the asylum now, before donning a golden, featureless mask. This person is Roger Hayden, better known as the Psycho-Pirate, and his golden mask is an artifact called The Medusa Mask, which allows its wearer to alter the emotions of other people. While he's better known to DC Comics fans as one of the few people in the DC Universe to remember the multiverse as it was before Crisis on Infinite Earths, Psycho-Pirate was originally an enemy of the Justice Society of America on Earth-2, who operated out of Gotham and most frequently fought Batman and the Alan Scott Green Lantern.
As the Arrowverse's heroes are trying to stop the rioting at Arkham Asylum, Caitlin Snow (later turning into Killer Frost) discovered a frantic woman in a storage room, muttering about how her cryo-stasis unit was shut down along with the locks, and how she needs to be kept cold, while trying to crack open a tank of liquid nitrogen. Though not identified by name, this woman is meant to be Nora Fries - the wife of Dr. Victor Fries, who was cryogenically frozen in order to save her life while he worked on finding a cure for the disease that threatened her life. While the details of this disease are rarely discussed in the comics, it would seem that this version of Nora Fries suffers from some form of mental illness, if only to explain why she's being kept on ice in Arkham Asylum.
As Nora Fries is digging around the storage room, viewers briefly see a familiar looking mask on one of the shelves. Film fans will recognize this as the mask worn by Tom Hardy in The Dark Knight Rises when he played the villain Bane. Sadly, for those hoping this means that the Arrowverse is the same reality as Christopher Nolan's movies, the circumstances surrounding Bruce Wayne and Batman's disappearances were significantly different from one another - and everyone knew Batman existed in those films.
Dr. Victor Fries / Mr. Freeze
When Nora Fries' actions accidentally bring Killer Frost to the surface, she quickly moves to defend herself by assembling a familiar-looking gun that attaches to the can of liquid nitrogen she was trying to open earlier. Even before audiences see her using it to knockout Killer Frost with a blast of focused ice, it's clear from the label on the case - which reads, "Fries, V." - that this belongs to Nora's husband, Victor Fries, aka Mr. Freeze.
Dr. Jonathan Crane / The Scarecrow
When Green Arrow and The Flash come to Killer Frost's rescue, Oliver Queen throws a lightning bolt at Nora Fries that rebounds and breaks a box full of test tubes that are labeled as the property of "Crane, J." Soon Oliver and Barry find themselves in a cloud of fog and suddenly fighting one another's worst enemies - The Reverse Flash and Malcolm Merlyn (played by John Barrowman). Fans of the comics will recognize the box as belonging to Jonathan Crane, aka Scarecrow, and the test tubes as being full of his infamous Fear Gas, which causes people to hallucinate their worst fears coming to life.
Dr. John Deegan / Doctor Destiny
By the end of Elseworlds, Dr. John Deegan has been left a desiccated husk of the man he once was, and locked in a cell at Arkham Asylum. This gruesome fate, coupled with his utilization of an artifact called The Book of Destiny, seems to affirm his status as an adaption of the villain Doctor Destiny. The comic book version of Doctor Destiny, who was a scientist named Dr. John Dee, had the power to bring dreams to life and alter reality on a small scale. While Doctor Destiny was originally a Justice League villain, he became more famous for his association with Arkham Asylum, having been portrayed as an inmate there in two classic comics - Grant Morrison and Dave McKean's Arkham Asylum: A Serious House on Serious Earth and the first book of Neil Gaiman's Sandman, Preludes and Nocturnes.