The Joker saw Barbara Gordon (whom he shot and paralyzed for life) briefly when she interrogated him and didn't recognize her. He even asked her if he had put her in that wheelchair. Later, he met her AGAIN and didn't recognize her, though he was impressed by her complete lack of fear in facing him. Babs wondered to herself if he's killed so many people it had just blurred together. Hours later, on his car ride back from town, it finally came back to him, and he immediately turned around to torment her further.
There was a time in The Batman Adventures when a reformed Harvey Dent was put through hell by the Joker. For Batman and Harvey, it was a moment of disaster, chaos and heartbreak. The Joker only did it "Because it was Tuesday."
Spider-Man once faced a guy called "The Master of Vengeance" seeking revenge because Spider-Man put him in jail for dealing drugs. Peter, who does that sort of thing all the time, didn't remember him at all.
Spidey had this as well with a villain called the Slyder, who THOUGHT he was the Unknown Rival to Spidey, but didn't even register on his radar. Only after fighting for a solid 10 minutes does Peter remember his gimmick, and then easily schools him with the exact same effort as before. Being remembered by Spidey has Slyder squee though.
At the "Light the night" trilogy, Spidey, Electro and a third incidental crook struggle with their own inequacies. The small crook really has if for Spidey because he never seems to remember him, even when he has arrested him three times. He bores a barman to death telling him this story several times.
A more famous example is Eddie Brock, a.k.a. Venom. Peter knows him all too well now, but when Venom first unmasked, he recognized Brock only as a disgraced reporter whose picture had been in the papers. He'd never met the man and had no idea he blamed Spider-Man for his ruined career.
After Spidey's unmasking during Marvel's Civil War event, the Chameleon hired a bunch of lesser known members of Spidey's Rogues Gallery and set them on the already beleaguered hero. When Will O'Wisp makes his grand entrance, Spidey pretends like he doesn't recognize the poor guy. Or at least he claims in his thought captions to be pretending. Honest!
Parodied by the second X-Factor team; three rather random villains died without X-Factor ever actually encountering them, and were resurrected by Charon as X-Factor's "greatest, and deadliest enemies!". To which X-Factor replied "WHO?!", "Only WE could have a bunch of "greatest enemies" that we never heard of!" and continued with several Genre Savvy quips about them being mistaken for X-Force, or the one team without action figures.
Invoked: Dredd is held at gunpoint by a woman whose husband he once arrested, but he tells her that he arrests a lot of people and can't be expected to remember them all. However, it turns out that he does remember, and he was just playing for time.
This trope was played for real when Whitey, the first perp we get to see Dredd arrest in the comics, escapes from captivity in the 10th Anniversary story with nothing but a grudge against Dredd on his mind. However, Dredd has no recollection of the man at all.
"Who the hell was Whitey?"
And in a similar later story, Bert Dubinski, the very first guy Dredd arrested back when he was still in training, is released from prison after thirty-five years and seeks Dredd out, believing he must have some significance to the lawman. He does not respond well to finding out Dredd regards him as just another criminal.
Used rather darkly in Transmetropolitan when Spider, the Anti-Hero protagonist, is revealed to have left one of his previous assistants before he left the City in a bit of a fix by being grossly negligent or uncaring (or, considering it is Spider, both) — a seedy bar was using mood alteration devices to create illegal orgies and filmed their customers. Spider went undercover to reveal it, but only cared to protect himself, neither protecting nor warning said assistant. The results went about as well as expected for her and she's carried a grudge ever since. Spider doesn't recall her name when prompted about the event and doesn't seem to care.
Mister Rictus has hints of this in Wanted. At one point his mooks murder a boy's parents in front of him, and he orders them to leave the boy alive; his explicit hope is that the boy will swear himself to vengeance, and "give me someone interesting to fight in my old age." It's implied he does this sort of thing a lot.
In the Iron Man storyline Armor Wars II, we see a revenge-driven genius named DeWitt mastermind Tony's near-destruction. We had never seen the guy before, but the big surprise was that Tony hadn't either — when the dust cleared and he finally got to see his dead enemy's face, he didn't recognize it. Over the next few issues, Tony was actually quite shaken over this. He'd never wanted to be an industrial shark, crushing opponents without even knowing it. (This was the whole point as far as writer John Byrne was concerned, but fans must have complained, because DeWitt was gratuitously brought back later for just long enough to explain why he hated Tony.)
Another heroic example happens in the Nikolai Dante story "The Memoirs of Nikolai Dante". After Nikolai finishes telling Odessa his life story, a guy with a gun bursts in, ranting about how Nikolai ruined his life. Nikolai is at first nonplussed, and when the guy explains that Nikolai killed his comrades and ran off with his girlfriend, Nikolai responds that that sounds like the sort of thing he would do, but the guy would need to be more specific.
Anti Heroic example: In the penultimate issue of Garth Ennis' Punisher MAX "Widowmaker" arc, Castle is rescued by a woman who explains that she did it because Castle killed her brutal mobster husband who beat and raped her and let his friends beat and rape her... Let's just say that she was really grateful for that slaughter in the first issue, as she knew for a fact she didn't have a chance in hell of pulling it off herself.
And in the final issue of Ennis' run, Castle is outmaneuvered and captured by a Special Forces unit. Turns out that its commander, ColonelHowe, owes Frank his life - he rescued a teenage Howe from a Viet Cong camp during the war. To Castle, it was just another of his countless deniable operations. To Howe, it was the most important moment in his life - the reason he joined Special Forces in the first place. This is why he volunteered to take Castle alive, and upon discovering that the generals who ordered him captured were monsters, he freed Castle and let him kill them all.
A classic and iconic Punisher example: Though he had good reason to know him later on and perhaps recall his origin, the first time Frank encounters Jigsaw (in the company of Spidey and Nightcrawler), Jigsaw describes his reasons and origins, and Frank, at that time a lot more social towards other justice-types, says to the others it's a pity he doesn't remember this guy at all.
Every mook in the demon Oliver's army in The Punisher: Purgatory is made from bad guys Punisher killed. They frequently bring this up when they fight him, and he denies any recognition. Except for Olivier's human form Frank Costa, as he is the one who got his family killed.
Becomes a major plot point in the Star Wars comic story "Jabba the Hutt: The Gaar Suppoon Hit." First Jabba made a (phony) bomb threat against his rival Gaar Suppoon's palace, knowing that this would cause Gaar to hire Imperial bomb specialist Kosh Kurp to come to the palace to inspect it for bombs. Then, while attending a business ceremony at Gaar's table, he reveals in front of Kosh that Gaar had once gone by the false name of "Sonopo Bomoor." This causes Kosh to realize that the very man who has hired him was responsible, many years earlier when Kosh was a child, for sacking Kosh's hometown and having his parents tortured and executed in the town square, forcing Kosh to watch the whole thing and then leaving him alive. But Gaar Suppoon had not recognized Kosh Kurp when he hired him; in fact, when Kosh angrily tells him "I was there," Gaar at first thinks that Kosh must have been one of his own soldiers! Long story short, Kosh kills Gaar in revenge and takes over his criminal empire, much to the delight of Jabba, who had always hated Gaar and who had known the whole story when he set the plan in motion.
One issue of Wildcats takes place billions of years in the future during the end of the universe. By this point the only living beings are a small group of gods and immortals, including SupermanExpy Majestic and Manny Weiss, the Wandering Jew. At the start of the story Majestic briefly reflects that he spent some time on Manny's home world, but neither can remember what it was called, they're sure it started with an "e".
One Red Sonja comic had this: A mighty warlord is after Red Sonja because her troops fought off his several years ago, and she personally cost him his left eye. (How he pulled through after that wound...) When they meet in a duel because of a city she's defending, he's furious when she tells him she doesn't remember him at all. She says this twice. And he cheats to win the duel.
In Terry Moore's Echo, NSB agent Ivy Raven is confronted by the remains of Hong Liu, one of the villains she shot and nearly killed earlier in the same story, and when he begins raging at her, she tells him "I've burned so many psychos, kinda hard to tell you guys apart."
In The Adventures of Superman Annual # 1 (1987), Superman fights an alien who has removed the brains of everyone in a small American town (while keeping the brains alive). Superman defeats the alien (who escapes), but is unable to return the brains to their bodies. The still sentient brains all commit mass suicide in horror of what's happened to them. A year later in Comic-Book Time, during Superman's self-imposed exile in space, Superman has another run-in with that alien, who doesn't even remember Superman at first...because what that alien did to that one small American town is something he's regularly done to whole populations of entire planets, both before his first encounter with Superman and since then!One would think that being forced to flee by Superman would've made an impression, even if his atrocities on Earth weren't memorable to him.
The Authority: Kev opens with SAS commando Kev Hawkins being cornered on the toilet by two men intent on killing him. They're IRA terrorists out for revenge, because Kev killed their comrades and brothers during an incident in west Belfast. Kev hasn't the faintest recollection of this mission, and doesn't even recognize his assailants' faces. He even uses "Sorry, mate. Still don't remember" as a Pre-Mortem One-Liner.
This trope is Mother's Milk's motivation in The Boys. He and his brother Michael suffered non-beneficial mutations from Compound-V that had been deliberately introduced into their mother's workplace, leading their father to sue Vought-American for damages. The lawsuit takes a massive toll on his father, but eventually, they manage to win a suit with Vought's deck stacked heavily against them. The victory is rendered hollow for MM however, when he overhears Vought's lawyers cheerfully brush off the case which crippled him and his brother and nearly killed his father of stress as "You win some, you lose some."
Inverted with a helping of Genre Savvy by Melaka Fray in Joss Whedon's comic Fray. When Mel was a little girl, she and her fraternal twin brother Harth were attacked by the powerful vampire Icarus. Harth was killed, and only by luck did she survive. Since then she's dreamed of revenge, but when she encounters Icarus again and he not only knows her, recognizes her despite being a grownup now, and is aware that she's the Slayer, (something Mel only just learned about) she takes that as a sign that something weird is going on. As she says, she and Harth should have been nothing to Icarus, just another victim in a lifetime full of them and forgotten by the next day. Sure enough, Harth was turned into an Undead Child and has become the Big Bad, while Icarus is his dragon.
A fairly rare heroic example: In Titans story tying into the "Planet DC" event, Bushido is cornered by bunch of Yakuza gunmen. Their leader wants revenge for his father's death at Bushido's hands; Bushido not only doesn't remember killing that specific mob boss, he thinks it's stupid of the grieving son to assume he would.
Another heroic example, in the Hell Boy short story "Act of Mercy", Hellboy is summoned by Dyavo Mahr for a rematch having defeating him once before. Dyavo carries on about their battle being one of legends, but Hellboy doesn't recognise him and dismisses him because of how weak and powerless he is. Eventually Hellboy sees what Dyavo really wanted from their second encounter having fallen so far from what he used to be, states that he is too much of a threat to live, and puts him out of his misery
Imagine what would happen if hundreds of regular, non super powered, run of the mill Mooks that Batman took out on a nightly basis decided they wanted payback and formed an entire army, lead by a guy who built himself a suit of armor to fight the Bat with? That's the basis of the character Terminus and his followers, the "Scar of the Bat". They aren't even really supervillains. They're just the regular criminals that Batman beat the crap out of and sent off to the police. Their nicknames are all based off the injuries Batman gave them. Like one guy named "Bootface". And the leader, Terminus, who was beaten in such a way that it caused him to develop a rare, terminal disease. During meetings with his henchmen, he acknowledges the fact that Batman probably didn't even give them a second thought at the times he first defeated them.
Deadpool: The Good, the Bad and the Ugly has yet another hero-to-villain example in the case of "The White Man". In the seventies, the Heroes for Hire and Deadpool took down this unfortunately-named pimp slash mob boss by turning his petrification powers back on him. Needless to say, when he's finally unfrozen forty "years" later, he's a bit pissed. He's even more pissed when he finds out that none of them remember who is or have any idea why he's so mad at them.
In James Robinson's current run of Fantastic Four, a mysterious villain known as The Quiet Man has been doing everything in his power to ruin the Richards family. When Reed finds out who he is, he's confused. He's even more gobsmacked that the villain's motivations for this is because Reed ended up winning over Sue Storm the day the guy decided to get the balls to finally talk to her.