1. Joker. To no one's surprise, The Joker is the best of Batman's villains.
Ra's Al Ghul found out about Batman's identity as Bruce Wayne by following his money. Ra's Al Ghul knew that Batman had to be very wealthy to afford to spend so much money and resources fighting crime, and to have all the tools that he does have.
However, through his own actions, Batman has proved a surprise villain, KGBeast, is actually who he seems to hate most, as he bent his iconic no-kill rule and left him for dead on multiple occasions.
Darkseid Respects Batman's Ruthlessness
It's a very telling statement by Darkseid, who respects Batman's willingness to sacrifice others for his aims more than Superman or Wonder Woman's raw power. He also suggests this is a trait particular to humanity, suggesting a kinship between the god of evil and the human race.
In Final Crisis, Darkseid was revealed to fear the New Gods' version of Death, as they represented a real possible end to the powerful villain's dominance in the DC Universe and an end to his evil reign.
6 Wonder Woman
She's been a loyal teammate, a close friend, a rival, and occasionally a romantic partner. Yet she has never found herself ever fearing Batman. It's not because she is an all-power Amazon with the blood of the gods running through her veins, although that certainly helps.
This raises the question as to why Batman was scared of Lex Luthor specifically. The reason Batman's other villains can't compare is that Lex Luthor is the literal foil to Bruce Wayne. Bruce's greatest fear is becoming the very evil he fights against every night, which explains Batman's no-kill rule.
Professor Hugo Strange. Hugo Strange's enmity with the Dark Knight stretches back to 1940, making him Batman's first major villain. He's a psychologist and chemist who knows Batman's not-so-secret identity.
No matter the media, the Joker remains Batman's greatest nemesis. On film, Jack Nicholson's Joker set the bar for villainy in Batman.
The Joker
Throughout their storied relationship, the Joker has known Batman's true identity and has chosen to ignore it. He simply can't bring himself to care about Bruce Wayne the human.
1) The Dark Knight Metal Batman Who Laughs unleashes the ultimate evil. In the DC Comics event Dark Knight Metal, Batman Who Laughs orchestrated a sinister scheme to plunge the multiverse into darkness. As part of his plan, he created a collection of evil versions of the character unleashed to carry out his bidding.
Very few villains actually respect Batman enough to pay their respects to his dead body. Most would dance happily.
“Have you ever danced with the Devil in the pale moonlight?” This quote from “Batman” (1989) will ring true with the Joker, a character from the DC Franchise first introduced into the Batman comics in 1975 as a supervillain.
To Be Forgotten. While fans got to hear many memorable quotes from Joker in Batman: Arkham, the series also revealed what his greatest fear is supposed to be. As it turned out, The Joker feared being forgotten more than anything else because it meant nobody was afraid of him anymore, rendering all his crimes void.
The revelation came in the pages of Detective Comics #1017, in which orphan Miguel Flores, having been rescued by Batman and Robin, tells the Dark Knight that his favorite superhero is Superman. Batman reveals that Superman is his favorite too.
Bruce Wayne
Their friendship goes back to Harvey's first appearance in Detective Comics, in which Batman refers to him as his friend and emotionally asks him to give up his life of crime. Because of this relationship, Two-Face is one of Batman's most personal enemies.
In Batman's origin story, Joe Chill is the mugger who murders young Bruce Wayne's parents, Dr. Thomas Wayne and Martha Wayne. The murder traumatizes Bruce, inspiring his vow to avenge their deaths by fighting crime in Gotham City as the vigilante Batman.
There's no doubt that recalling the fate of his parents is Bruce's biggest fear and regret. No matter who kills Batman's parents in different media, it's the catalyst to the person he becomes. Bruce spent all his childhood and early adulthood scared of remember what had happened.
Batman has fought numerous villains in his time as the Caped Crusader, but few have harmed him and his allies as much as the Joker has. Batman has admitted several times that his enemies don't get worse than the Joker, so it's obvious that the clown has left a deep scar in Batman.
Wayne's phobia of bats is the most apparent. It stems from his childhood incident of falling down a well with bats flying up above him. Because the incident happens at such an impressionable age, it causes extreme fear and becomes impossible to get rid of.
Catwoman's deep-seated fear personified by Batman really reveals more about her own psychological hangups than a terror fueled by the Dark Knight; she wouldn't flirt with him so aggressively if she was genuinely scared of him.
Bruce Wayne's Batman hates Superman simply because he exists and his battle with Zod destroyed Wayne Tower in Metropolis. He fears that the alien won't be able to be controlled and therefore, should be murdered.
While Darkseid was fighting Zeus, Ares landed a powerful blow to Darkseid, breaking the latter's spear and wounding his shoulder. The wound caused Darkseid to faint and his parademons had to take him back to his ship.