Eighteen years after their creation, it was revealed that AvengersScarlet Witch and Quicksilver were actually the children of their former leader, long-time X-Men antagonist Magneto. Their feelings over this revelation were mixed, to put it mildly. Still, as Magneto is a Drama Queen, he did not told this directly. He told that Luna was his granddaughter, and let them react to that.
Polaris, of the X-Men, was revealed early on to be Magneto's daughter, too. But then that was revealed to actually be a plot by the villain Mesmero, who was using a Magneto robot to make that claim. Then later it was again revealed that she is his daughter... then once again not. Currently, she is once again revealed to be Magneto's daughter... ugh.
This also occurs in a prequel tie-in to House of M. Polaris, Quicksilver and Wanda (she's not the Scarlet Witch, long story), are Magneto's loyal lieutenants throughout his campaign to Take Over the World and he keeps the fact that he's their father from them the whole time, although ironically he acts more like a father figure to all of them than in the mainstream universe; they assume he just sees them as like his children. When victory is achieved he reveals the truth and they are... not pleased, since their lives between him abandoning them as babies and them joining his army as adults were pretty rough and they could have really used a father growing up. They also don't look kindly on his explanation that it was to protect them.
The Incredible Hulk: Hiro-Kala knew that he was the son of the Hulk. He didn't know that Bruce Banner was the Hulk. So when they first met, the following exchange happened:
During John Ostrander's run of The Punisher, Jigsaw has kidnapped the member's of a mafia family that Frank has fallen in with. While talking with the oldest sister, he tells them why he's doing this; he and Frank are cousins. When they were kids, Frank was always showing him up, and everyone loved him. When she asks him if it's true, he says nah. He was just lying to pass the time.
A pivotal turning point in the original Spider-Man 2099 run featured Miguel O'Hara (Spider-Man) discovering that the main antagonist of the series and head of the megacorp Alchemax, Tyler Stone, was in fact his father. This derailed the current plotline for quite a few issues as Miguel wrestled with his hatred of the man. The trope was lampshaded near the end of the title's run, when Tyler attempted to shock Miguel into following his orders by dropping the bombshell of his parentage, only to have Miguel, who by this point had come to terms with the fact, casually sip his coffee and then smugly and calmly reveal that he knows.
Tyler Stone: And you will do it... because I'm your father. Miguel O'Hara:[sips coffee] Yeah, I know. Tyler Stone: You... you know? Miguel O'Hara: Yeah. Now get out of my office... dad.
Mr. Sinister pulls a particularly unpleasant version on Gambit in X-Men: The End when he reveals that Gambit is a clone created from Sinister's original DNA mixed with that of Scott Summers. Thankfully, this probably isn't canon — the Summers have a messed-up history as it is.
Speaking of the Summers family, several years after his introduction, Cable was retconned as being Nathan Summers, Cyclops' baby son who he'd previously been forced to send into the future to save his life. What happened was in the Bad Future Baby Nathan grew up oblivious to his parentage and eventually time-traveled back to the present, though by that point he was older than his father.
Thor gets this in The Avengers (2021) "Enter the Phoenix" arc. The mutant cavewoman/Phoenix Force avatar, Firehair tells Thor that Odin hid the truth and she's his real mother. Thor does not take this well, and Tony, who's had his share of unsettling parental reveals, mumbles, "Why can none of us just have nice, normal parents?"
In their Star Comics' imprint Planet Terry series, the Big Bad Vermin the Vile gets Terry, who has been searching for his parents throughout the galaxy, to believe that he is actually Terry's father. However, it is later revealed that a villain known as The Hood, who is about the same age as Terry, is actually Vermin's real long-lost son.
◊ With Peter distracted, Mysterio proceeded to kick him in the nads and made his escape as his nemesis was hunched over in understandable agony.
