The original Gen¹³ had more of a "Luke You Are His Father", with Burnout and team mentor Lynch simultaneously learning that the former is the latter's long lost son.
Gen-Active revealed A. Sublime of DV8 isn't adopted, and B. her biological father is Michael Cray, alias Deathblow, one of the most prominent figures in the Wildstorm universe. Notably, it's revealed to the reader, but not necessarily the characters — Sublime's mother doesn't seem to remember his name.
In the first G.I. Joe comic series, a boy named Billy living in the Cobra-controlled town of Springfield had joined the local anti-Cobra underground, believing that his father had been swayed into joining the organization by Cobra Commander. He'd failed to realize that his father was Cobra Commander all along. Destro knew the truth, however, and revealed it when he intervened to stop Billy from assassinating the Commander.
Knuckles' girlfriend Julie-Su discovers that she's the half-sister of Dark Legion leaders Kragok and Lien-Da, which also makes her a descendant of Knuckles' ancestor Dimitri (making her and Knuckles very distant cousins). And sometime later, it's revealed that Remington is Kragok's son.
In a dark alternate universe, 30 years in the future, Lara-Su was raised to believe her father Knuckles had been killed by Constable Remington. However, after she goes back in time (and travels to the wrong dimension too), her mother Julie-Su finally tells her that, in fact, Knuckles wasn't killed by Remington, but went insane with Chaos Powers and became the dreaded leader of the Dark Legion and by extension tyrant of the entire planet, Enerjak.
Star Wars: Darth Vader shows the inverse in issue #6: Boba Fett reveals to Vader that the boy who destroyed the first Death Star was named Skywalker. After Fett leaves, there's an Internal Reveal flashing back from the end of Revenge of the Sith to a little after A New Hope (to Luke and Vader's first confrontation in a previous comic). Vader is mostly silent, but his hand is shaking with enough Force energy to shatter the glass window in front of him.
Vader: Skywalker. [Later — Vader folds his arms. Scenes flash in his memory. Padmé crying. Padmé's funeral. The destruction of the first Death Star. His first confrontation with Luke.] Vader:I have a son. The glass before Vader is almost completely gone now. Vader: He will be mine. It will all be mine.
At the end of the canon comic series Darth Vader: Dark Lord of the Sith, Vader undergoes a series of dark side visions relating to his past, present and future. One of these visions heavily implies that Palpatine himself was responsible for Anakin's conception through the Force (and thus tying back to the revelation that was planned to originally occur in Revenge of the Sith).
In Issue 6 of the Dallas arc of The Umbrella Academy, it's revealed that Number 1 and Number 5 are biological siblings (they were adopted siblings before this point).
Tossed in a blender with Luke, You Are My Father (but not really) in Usagi Yojimbo: Usagi discovered that his old flame Mariko's son Jotaro is actually his son, and Mariko's husband (Usagi's very unfriendly rival) also knows but loves Jotaro anyway. Usagi and Jotaro's sword master guessed almost immediately (they're very much alike), and gives them the opportunity to travel together for several months; after talking with Tomoe about responsibilities and relationships, Usagi decides not to break the bond between Jotaro and his family, while Jotaro decides not to force Usagi to give up his wanderer lifestyle to take care of him. It turns out Mariko told Jotaro the truth, but left out the part about Usagi knowing too. Upset at his "weakness" and the fact that he doesn't know when or if he'll ever see his "uncle" again, Jotaro calls out "Miyamoto Usagi! You are my father!!" but Usagi is already too far away to hear ("Just a trick of the wind, I must be tying my ears too tight"). TL;DR: Father A and Son B know they're related, but they don't know the other knows the truth (C,D,E, and F know the truth too but they aren't talking, mainly out of respect).
In Lori Lovecraft: Into the Past, R.C. learns that his mother is 60s star actress Danke Schoen, who was forced by the studio to give up the baby for adoption to avoid a scandal.
