Batman: In The Killing Joke, The Joker's three dwarf henchmen just disappear after Commissioner Gordon is put in a cage; they aren't seen with the rest of the circus freaks, not even when the appearance of the Batmobile scatters the freaks away.
Planetary: An early issue has the team invading a secret installation where scientists are attempting to create a fictional Earth and give it substance. They succeed, but someone escapes from the fictional Earth and goes on a killing spree. The issue ends with a caption telling us that he is still at large. He is never seen or mentioned again, except for a quick mention in the final issue, where Elijah basically says they've given up on looking for him.
In Mark Waid's mid-00s reboot of Legion of Super-Heroes, the first arc's villains were a group of psychopathic, xenophobic Daxamites. (Daxamites are related to Kryptonians, each one roughly as powerful as Superman.) To underscore how powerful and awful these villains were, a dozen of them destroyed a planet in minutes by flying over it and blasting it with their heat vision. Those are the key facts: very evil, very powerful, and there are (at least) twelve of them. The next issue four of them attack Earth and it's an amazing fight, with heroic sacrifices and deaths, and at the very last moment the four Daxamites get defeated, the Legion proves its worth to the skeptical authorities and the universe rejoices. And the other eight Daxamites? Each with the power to destroy a continent? Responsible for the deaths of billions? They never get mentioned again.
At the beginning of Superman's Return to Krypton, Superman goes into space to confront a monster which is not only planet-sized but also super-fast. After said creature unintentionally causes Superman to time-travel, thus kicking off the real plot, it's never seen or mentioned again.
In the "Secret Identities" story, a Kryptonian woman reproaches Supergirl for blowing her and her son's cover, flies off and is never seen or mentioned again. Did she manage to blend in among humans again? Was she found and "purged" by Sam Lane's troops at the climax of New Krypton? Nobody knows.
Superman: Birthright: Lana Lang is noted to have disappeared from Smallville at some point before the beginning of the story. That element never comes up again, and the only other appearance she makes is during a flashback to when they were in highschool.
The Return of Superman 1993 trade paperback terminates during the beginning of Adventures of Superman #505, ending with Superman reuniting with Lois Lane without bothering to address Clark Kent's reintroduction into society.
Adventures of Superman #431 introduced the villain Constantine Stratos, an insane Greek millionaire who fancied himself the scion of the gods of Olympus and used a Weather-Control Machine to attack Superman. Superman destroyed the machine, but was not able to save Stratos, whom he believed was killed when his machine exploded. The end of the issue revealed that Stratos was very much alive and had been altered by his exploding machinery so he now could manipulate the weather by himself, without his technology. He was last seen swearing vengeance on Superman. This was in 1987, and he was never even mentioned again... until 2005, when he appeared as a character in the novel Superman: The Never Ending Battle, by Roger Stern.
Superboy (1994): In the second annual, Superboy, Cadmus' thirteenth attempt at cloning Superman, is introduced to the prior twelve who are all in stasis pods deep inside Cadmus. While attempt one dies during the issue and another was already dead due to his pod being destroyed the rest of them are apparently stuck in these pods forever as they're never seen or directly mentioned again.
The second iteration of the Newsboy Legion, all of whom but one are Cadmus created clones, disappears even before the originals are murdered. In New Krypton, Jimmy Olsen asks Guardian, who was the legal guardian of one of the kids and Parental Substitute to all of them, where the Newsboys are following the dissolution of Cadmus, Guardian says that even he has no clue what has become of the kids. For all he knows, they have been killed and put into test tubes by the military.
Crucible: Two members of Roho's villainous squad, Rendll and an unnamed robt, completely disappear from the story after getting wounded and damaged, respectively, by Maxima during the second battle between both groups.
The Killers of Krypton: After Kara manages to escape from Mogo, Salaak is determined to hunt her down and arrest her, but neither nor the Green Lantern Corps are seen again.
Starfire's Revenge: Rodney Marlowe is not mentioned again after Supergirl busts Starfire's European operation, despite previously being eager to avenge his brother, who had been executed by Starfire.
The Girl with the X-Ray Mind: Dick Malverne spends one whole issue trying to prove that Lena Thorul is Supergirl; but as soon as he gets a "confession", he is dropped from the story.
Way of the World: Once he gives a blood sample for attempting to cure a sick child, Resurrection Man is completely dropped from the story with no explanation.
In the Escape from the Phantom Zone crossover, Supergirl and Batgirl break a cryokinetic guy called Caleb out of his cell in a Project Cadmus black site and make off with him. When they meet later, neither of them mentions what happened to Caleb after their flight.
In Superman/Supergirl: Maelstrom, Superman says he asked Power Girl to watch over Metropolis while he took Supergirl on a training space trip, but she fails to show up when the Female Furies arrive in the city and go on a rampage.
The Super-Revenge of Lex Luthor: The two unnamed mooks who were working for Luthor in the first two issues are conspicuously absent in the final one.
Supergirl (1984): When Nigel drops by Selena's den, he runs into a crowd of partygoers eating and drinking. Selena claims they are members of her newly-created mook army. However, they are not mentioned again, and they are not present during any of the battles between Supergirl and their mistress.
In The Earthwar Saga, the situation is so dire, and the Legion is so short of manpower which they cal the Legion of Substitutes and even retired Legionnaires...except Supergirl, who could have greatly helped but is not even mentioned.
DC Retroactive Superman: After figuring prominently in the two first issues, Supergirl is completely and noticeably missing in the final one, not even meriting one mention.
In crossover "Fate Is The Killer", Prince Adam is attending a royal feast together with his parents and Man-At-Arms when Zodac bursts into the place. Teela and several guards rush into the scene, and Adam takes advantage of the mayhem to go out of the castle and turn into He-Man. Before He-Man can return, though, he is intercepted by Zodac, and the story did not explain what happened to He-Man's parents, mentor and love interest after he left the feast.
"The Super-Duel in Space": In order to escape from the Bottle-City of Kandor, Superman entices a Kryptonian metal-eating mole to eat his way through the metal cap. After the mole has burrowed one tunnel through the metal, Superman flies off, leaving the mole behind, stranded on the top of the giant bottle. It is unknown what happened afterwards to the animal who helped Superman beat Brainiac and save the Kandorians.
Lucifer: Elaine's friend Mona falls increasingly to the background as the story progresses, and by the end she's not present for any of the important events, and no-one even mentions her. Considering that Lucifer had made her a guardian spirit (of hedgehogs!) in his Creation, you would think that she would pop up at some point, or at least warrant a comment.
Green Lantern: Rebirth doesn't provide any explanation for what Hector Hammond has to do with the plot. He appears for a page at the beginning detecting that Kyle has brought Hal's inanimate body back to Earth. Then he appears near the end picking up that he's back as a Green Lantern and laughing about it.
Blackest Night: In the tie-in Green Lantern #47, the action on Ysmault cuts away after the Black Lanterns' failed attempt to kill Atrocitus. At the end of the issue, Atrocitus suddenly appears on Okarra, with no indication of what happened to the other Red Lanterns, or the "Lost Lanterns" who had also been on Ysmault. The Lost Lanterns reappear after the event no worse for wear, but they never say what happened.
Brightest Day: Hector Hammond's fate after joining up with Krona and his subsequent bond with Ophidian. Last we see of him, he and Krona head off to parts unknown, and in subsequent issues, Krona and the Entities (including Ophidian, who has split with Hammond) arrive on Oa. Is he back in prison? Dead? Roaming free? Who knows.
In Sensation ComicsSteve Trevor's secretary Lila Brown makes a few appearances before disappearing without explanation. Later on in Wonder Woman #12 a villain named Nerva acts as his secretary for a single issue, still with no explanation for Lila's disappearance.
In the Volume 1 arc Judgment In Infinity Wonder Woman summons the League for a debriefing, Superman and Green Lantern go out to look up information in their archives about the Adjudicator... and then the Leaguers disappear from the story. Shortly after, Diana summons an army of heroines to fight a multi-dimensional war, but she does not even think of calling Mary Marvel or Batgirl.
Wonder Woman (1987): The Widow Sazia was last seen winning the brutal Mob War that tore Boston apart and having killed her last rival, after making it clear her enforcers are cybernetic, she's got a portal that allows her to pull in superpowered help from other dimensions and she's way too clever and forward thinking to be picked up by the regular police.
Lampshaded and deconstructed in the Grant Morrison run of Animal Man. One of the first big hints that something is very wrong is when Animal Man notices that a group of criminals who threatened his wife seem to have just inexplicably disappeared after their subplot ended, with no evidence of a trial or anything even though they were arrested for attempted rape and murder. Later on, he discover the existence of the "Comic-Book Limbo" for this sort of character. Not dead. Not in prison. Not retconned out of existence. Just gone, existing in a limbo of continuity and non-continuity until some writer decides to bring them back.
JLA (1997): When a hostless version of the The Spectre went after Triumph, the League put him in their trophy room as a memorial for a fallen member — and then forgot he was there when the Injustice Gang blew up the Watchtower.
