The show is usually good with continuity, which makes this oversight all the more damning: In "FUGITIVE", the operatives and the head of decommissioning, #86, are going after an escaped operative, #208, scheduled for decommissioning. #86 briefly mentions sending their best spy, #362, to infiltrate the Delightful Children's mansion (where the #208 is entering). While inside, #208 escapes from #86 and was last seen running down the hall, then a similarly-dressed #362 runs back and is mistaken for him and captured. #362 became a major character in her own right, but the show never got around to answering what happened to the escaped operative.
In the episode "You May Now Kiss the... Uh... Guy Who Receives" Chris' romance with the blonde girl vanishes after she talks to Chris outside the City Hall.
In the episode where the Griffin house gets possessed by poltergeists, Herbert the Pedophile fights back against a tree demon who is about to eat Chris and the two (Herbert and the tree) fall to their dooms after the tree splits the ground open. On the TV version, this counts as a "What Happened to the Mouse" moment because we never see Herbert or the tree for the rest of the episode. On the season four DVD, however, there's an extra scene where, after Peter ditches the cursed skull in the trash as The Griffins drive away, Herbert and the tree come out of the hole and apologize to each other for fighting. Herb then invites the tree over to his house and asks him if he's a "giving tree" or a "receiving tree". Apparently, The FOX censors turned this Brick Joke into a What Happened to the Mouse? moment all because they didn't approve of the anal sex joke implied in the "giving/receiving tree" line, which is odd, because FOX let Seth MacFarlane and co. get away with pedophilia jokes centered around him (and some that aren't), though according to DVD commentary, the FOX censors have always been wary about Herbert the Pedophile note (particularly on the episode where Chris has to work for Herbert to pay off a broken window. There were a lot of scenes and lines of dialogue that the FOX censors asked MacFarlane and company to tone down or eliminate). This (from the episode "Petergeist") is just one of the many examples of how wary FOX is about him.
In another episode where Chris is put on a diet, Stewie gloats in front of him about being able to eat whatever he wants and consequentially gains a ton of weight and grows increasingly listless as a result. In the final scene with Peter in the hospital, Stewie is skinny again, with no mention of how he lost weight.
In the 1987 Teenage Mutant Ninja Turtles 1987 miniseries, Shredder mutates more punks after Bebop and Rocksteady lose their first fight against the Turtles. Then for some reason he doesn't do anything with them, and the viewers next see them in a jail cell in the Technodrome's portal room. You never learn what happens to them when the Technodrome is sucked through the reversed portal.
The Rat King made his appearance in the fourth season, battling to a standstill with Leonardo. After the episode was over, it was made clear that the Rat King had survived and that there was a strong possibility of him showing up again in the future. Three seasons later ("The Lost Season", "Fast Forward", and "Back to the Sewers"), the Rat King still hasn't made any appearances and is never mentioned again. For better or worse, the Rat King subplot is more or less dropped after his Season Four episode. A better title would be "What Happened to the Rat?" in this case.
What happened to the Rat King is answered in the "Back to the Sewer" season finale. Towards the end of the episode, he makes a cameo appearance, watching April and Casey's wedding from afar... The Rat King had promised himself that he would be watching the Turtles (presumably waiting for a good chance to strike). He was watching the Turtles when he was at the wedding. He probably had been watching them for a long time from off-screen.
In the Teenage Mutant Ninja Turtles special Turtles Forever, the 1987 version of April O'Neil was kidnapped by a giant mutant banana (don't ask) and no one knows what happens to her. Knowing 1987 April, the Turtles rescued her off-screen. That's what happens every episode, after all.
The Simpsons does this a lot. Whatever happens in the first act to get the actual plot running will never be mentioned again. Or if it is, it'll be to hang a lampshade on that the story's moved on and no-one's interested any more, like the badgers in "A Tale of Two Springfields".
Or the first part of "Tennis the Menace" where Homer buys a burial plot for Grampa Simpson, but ends up creating a tennis court in the backyard after a coffin salesman tells Homer that his backyard needs to be the size of a tennis court if he's thinking of burying Grampa there. Or the first part of "The Cartridge Family," where the plot goes from the family trying to survive a town-wide soccer riot, complete with fighting and houses being burned to a very special episode (a Simpsonized version of it, anyway) where Homer buys a gun for protection and drives Marge and the kids away because of how irresponsible he is with it?
The bagboy strike on "Simpson Safari" that was abandoned for yet another "The Simpsons are Going to [Insert Country/Continent/State Here]" plot. That episode hung a lampshade on it. After having lost their guide and become stuck on a boat floating down a river, Homer wonders if the bag boys have resolved their strike. The episode is later dedicated to the bag boys of America, "whose ineptness and greed were the inspiration for this episode".
In another episode, Apu takes a bullet for James Woods (It Makes Sense in Context), says his last words and then we see him make his recovery in a hospital along with Woods before the episode ends. The assailant, who could've very well shot again at his initial target, isn't shown again. Neither is James Woods.
In the episode where the Itchy and Scratchy producers are trying to introduce "Poochy", the show's new marketing-driven dog, a test audience sees Itchy and Scratchy driving to a fireworks factory. When they're about half a mile away from it, Poochy appears and begins doing all sorts of "cool" activities like skateboarding and playing basketball. Milhouse, who is watching the show at The Simpsons' house, screams "When are they going to get to the fireworks factory?!?"
In "One Fish, Two Fish, Blowfish, Blue Fish", Homer is diagnosed with death in 22 hours. Having nothing to lose, he accepts Ned Flanders' invitation to a barbecue he doesn't want to go to. But at the end of the episode it's shown that Homer survives. The last shot of the episode is him eating chips and watching TV; the barbecue is never mentioned at all. The commentary discusses a deleted final scene where Homer has to deal with all the consequences of what he thought was his last day alive: not only is he stuck at the barbecue, but his father now wants to spend lots of time with him rather than having accepting their distant relationship, and Mr. Burns has some harsh words for him after Homer insulted him.
After "Two Dozen and One Greyhounds", She's the Fastest just vanishes and is never mentioned again.
Also, in "Insane Clown Poppy" Krusty seems to have a pretty strong relationship with his daughter at the end, who just vanishes next episode.
In the episode "Like Father, Like Clown," Krusty's assistant, Lois Pennycandy obviously holds a torch for Krusty, but this has never been referenced or referred to again.
Herb Powell, Homer's long-lost half-brother appears in two episodes early in the show's run, "Oh Brother, Where Art Thou?" (Season 2, Episode 15) and "Brother, Can You Spare Two Dimes?" (Season 3, Episode 24). After the second, in which he regains the fortune of which Homer's blundering deprived him in the episode wherein we meet him, he all but vanishes. They later lampshade this, when Homer mentions in passing "my seldom-seen brother, Herb."
Apparently Marge and/or Homer still know where he can be contacted, they just haven't had a reason to in a while. In "Changing of the Guardian", (Season 24, Episode 11, 22 seasons after BCYSTD), they consider him as a potential guardian for the kids in case of their unanticipated demise, but discount him because he's poor again.
And in "Days of Wine and D'oh'ses" What Happened to the Bear? The commentators would also like to know.
The commentators also want to know what happened to the Scottish woman that Willie meets in the episode "Whacking Day."
In "Homer At The Bat", Ozzie Smith ends up visiting a literal tourist trap, the Springfield Mystery Spot, which turns out to be some kind of Negative Space Wedgie, and he promptly falls into it. In the snapshot at the end we can see his specter hovering over the rest of the group (presumably invisible to all save the viewers). We never find out if he managed to escape the Mystery Spot, so as far as we know he's still falling through space and time...
It is also never revealed what happened to Scorpio after taking over the east coast and giving Homer a Football team as reward for helping his scheme.
Viewers with long memories will remember "Bart Gets Hit by a Car", particularly the scene where Bart goes to Hell. The Devil looks him up on a computer and says, "You're not supposed to be here until the Yankees win the pennant again," and returns him to the world of the living. October 1996 came and went. Nothing. (Okay, in fairness, he thought it would take 100 years, but come on, not even a throwaway Brick Joke?) In the DVD commentary, someone says "Well, that didn't happen," and that's all anyone involved with the episode has ever said about it.
Remember Bart's Star Trek belt from the episode "The Homer They Fall"? Neither does he. The DVD commentary does make mention of how they pretty much abandoned the "Bart gets his Star Trek belt stolen" storyline for the "Homer becomes a boxer" storyline (which they also pointed out was a rehash of "Homerpalooza," only instead of Homer taking hits to the gut without feeling pain, it was hits to the head).
The first act of "Lisa The Greek" has a subplot about Bart going clothes shopping with Marge, getting embarassing clothes and ends with him in the car with the bullies outside waiting to kick his ass. It's never brought up again after that.
There's also the final fates of Smellerbee, Longshot, Long Feng and the Earth King.The Promise confirms the fates of three of those: Smellerbee and Longshot are alive, having reassembled the Freedom Fighters to protest the Fire Nation's occupation. We don't know how they made it out of Lake Laogai. Earth King Kuei is back in place as King of Ba Sing Se.
Where's Cabbage Man? WHERE?! Yeah, he was credited with helping with the ''accurate'' play about the Avatar, but can he sell his cabbages in peace now that the Avatar has no Fire Lord to deal with? The Legend of Korra reveals that he and/or his descendants started a very successful technology company, Cabbage Corp.
Not to mention, what happened to Foamy?!
The Legend of Korra Speaking of Book 1's finale, what happened to the Lieutenant? Betrayed by his bending boss and thrown in a corner, never to be seen again?
When Iroh reveals to Zuko that his maternal great-grandfather was Avatar Roku who was given the crown of the prince of the Fire Nation as a gift, Iroh then gives the crown to Zuko. It is never seen or mentioned again, and becomes somewhat moot when Zuko is crowned as Fire Lord in the Grand Finale.
You also don't know how Iroh gets the crown in the first place. It was buried during the volcano eruption. It is last seen hitting the floor after rolling off of a nightstand. Roku runs outside and stares at the erupting volcano for several seconds until his wife emerges from their house. She might have scooped it up to take it with her on the boat, but it is never shown or mentioned.
This is another one to go to the comics for, as it's revealed Azulon deliberately got his son married to Roku's granddaughter, to fulfill a prophecy.
Early on in "The Fortuneteller," Aang presents Katara with a replacement necklace he wove out of Sokka's fishing line. Shortly after, the necklace unceremoniously disappears and Katara remains bare-necked until her original necklace is returned.
Haru, Teo, and The Duke all but vanish during the "field trip with Zuko" episodes until they can be conveniently Put on a Bus in "The Southern Raiders".
Significant if only for a few characters, but what Katara did in The Southern Raiders was never followed up on. We don't see much of a reaction from Sokka, and none whatsoever from Hakoda. The last mention of Kya is when Hakoda says that she'd be proud of her children, and Katara getting teary-eyed and touching her necklace. Granted the finale had other things to deal with, but perhaps the wider context could have been dealt with better. Yes, Kya's death was a major part of Katara's Character Development specifically, but as Sokka admits to Toph, it (understandably) messed up their family.
Towards the end of Season 2, Guru Pathik moves into one of the old Air Nomad temples, and he tries to help Aang control the Avatar State, but Aang leaves without mastering the final chakra for the Avatar State. He's only referenced once in Season 3, and it's questionable as to whether or not it's a "real" reference as Aang was hallucinating due to sleep deprivation at the time.
Xin Fu and Yu's fates are left unexplored after Toph left them in the metal cage they used to trap her.
After his premature partial Heel-Face Turn left Zuko in an Angst Coma, Iroh tells him that "this fever is not a natural sickness" and that he will emerge from it as "the prince he was meant to be," which seems to suggest that there's more going on than mere stress, possibly something supernatural. However, this plot point is never elaborated, and Zuko returns to his jerk-y ways soon after.
Whatever happened to Sokka's Cool Sword after it fell off when Sokka threw it to save himself and Toph in the Grand Finale?
Azula is also M.I.A. as she was last seen running into the Forgetful Valley at the end of the Search (one of the comic). So far she has not been referenced in The Legend of Korra.
Her two lackies, Ty Lee and Mai are also never referenced in the sequel series. Fans will likely never know whether or not Mai is Izumi's (Zuko's daughter) mother or not.
Despite being a member of the Gaang and Sokka's girlfriend at the time, Suki is never mentioned in The Legend of Korra.
In the Transformers Animated two-part episode "Megatron Rising", the Dinobots appear in the first part, obviously hinting at an appearance in the second. Though the second part's main battle takes place on Dinobot Island, they are nowhere to be seen. This was explained in an interview with the story editor-originally they were going to be beaten rather easily by the newly resurrected Megatron. However, the animation of the scene was terrible. That, and they were afraid the fans would be upset (especially since it violated the character profile saying Grimlock was supposed to be as strong as Megatron.
By the Grand Finale, there are still several loose threads hanging, including where were Blackarachnia and Waspinator at the end of "Predacons Rising", did Ultra Magnus recover from Shockwave's attack, where did the protoform Sari used to be come from, as well as what happened to several characters who were simply absent in the end.
For example: Given the manner in which Starscream finally dies, a bit of info on the fates of Wreck-Gar, the Constructicons, and Slipstream would have been nice. Not to mention Soundwave. And Team Chaar. And Skywarp and Thundercracker. Yeah, Animated has a lot of this. But that's what you get when a show is canceled.
Thankfully, a few things do get explained in the two 'AllSpark Almanacs', such as the fact that Ultra Magnus was going to go offline in season 4, and that there was originally a scene cut from "Endgame", showing Slipstream bringing Starscream back online (somehow).
In an episode of The Proud Family, Penny befriends a Muslim girl and her family as part of a school project on racial diversity. One night, Penny and the Muslim family return home to find that someone scrawled a racist message on the garage door (in the original version, it read, "GO HOME, TOWELHEADS!"; in the reruns, the message was digitally altered to just read, "GO HOME!") and just before it cuts to a commercial, everyone looks shocked and horrified. When the show returns, the family is having dinner at a restaurant and no one mentions it again. Even though Penny does mention that Muslim people have been discriminated against more thanks to the 9/11 attacks and that doing so is wrong, the viewer is still left asking who scrawled that horrible message on the garage and why.
In Beast Wars, Airazor and Tigatron left to search out the downed stasis pods, then were captured by the Vok. While a few more stasis pods showed up, there were dozens that were never seen again. The IDW comics attempt to resolve the storyline of the missing stasis pods by having all the Transformers within emerge as either Maximals or Predacons thanks to the machinations of Razorbeast in a convoluted storyline involving time-space displacement and whatnot.
Considering that the planet that the series takes place on is 70% water, it wouldn't be surprising if a great many of them were crushed in the great pressures of the deep. Not to mention it is heavily implied that the "quantum surge" in the Season 1 finale destroyed or damaged most of the pods. The ones that created Quickstrike and Silverbolt were heavily damaged causing the scanner to fuse two beast modes together for them. More telling, early in Season 2 Rhinox comes across a "blank" stasis pod. This means the Spark of the protoform inside has been extinguished, meaning it is dead, which can lead the audience to assume the remaining pods that were not destroyed upon impact suffered the same fate. Rhinox basically says that as far as they know, all of the pods are dead after the surge. Tigatron and Airazor were going to go explore to see if there were anymore, but he didn't sound hopeful. Tigatron and Airazor never found any, so we can assume they all died except for Silverbolt, Quickstrike and Rampage.
One pod was found in season 3. It was a blank and Megatron used it to create Dinobot II, with half a spark of Rampage.
In The Animals of Farthing Wood, Fox and Vixen's second son Friendly played a major role in the second season also when he was introduced, during season 3 he appeared for the first three episodes then is missing for the rest of the series.
In series 2, both Mossy and Ranger have sisters who each stop appearing after an episode or two.
Stripperella: In "Curse of the Were-Beaver", Stripperella jostles Shaw the beaver hunter to stop him from killing the were-beaver, and he falls off the roller-coaster scaffolding, landing (off-camera) with a splat and several disgusted-looking onlookers. And... we never see what happened to him ever again, so either he landed in something icky that broke the fall, or the heroine callously killed a man for doing his job.
Stripperella was pretty much a part of an Animal Wrongs Group in that episode, so yeah she would.
Project Carthage is mentioned once at the end of Season 2 as Franz Hopper's former employer, possible origin of The Men in Black (who are themselves not explained) and motive for creating Lyoko and XANA... and is never mentioned again after that.
It's revisited in (and is the main focus of) the novels, thankfully.
Taelia. An exact doppelganger of Aelita, subject to many fan theories about her origins — but never mentioned after "The Girl of the Dreams". It's unknown whether she's still a student at Kadic (though quite unlikely).
The wolf motif in Aelita's nightmares, where they are often seen chasing her — or, for that matter, the whole sequence with wolves chasing Mr. Pück — goes entirely unexplained in the show. The second novel reveals that (in this universe, anyway)the wolf visions stem from Aelita's residual memories of Anthea's kidnapping, wherein Aelita was menaced by Grigory Nictapolus's Rottweilers, Hannibal and Scipio. Of course, Rottweilers and wolves have vastly different appearances, but it's wholly possible that, at age four, Aelita simply remembered the menacing dogs as wolves.
More minor example — In "Double Take" at the end of the battle between Yumi and a XANA-possessed William, William has Yumi cornered with his sword. He then lowers it, approaches her, and begins stroking her face. Yumi pulls his hand away, and William pushes her off the cliff. The incident is neither explained (Trickery on XANA's part? William resisting XANA's control?) nor mentioned again.
Not so much a "what happened" as a "what will happen" in the case of Ahsoka in Star Wars: The Clone Wars. She's neither seen nor mentioned in Star Wars Episode III (which The Clone Wars is a prequel to), which is understandable as she's a brand new character created for the series. However, that implies she's either dead or Put on a Bus, thanks to the Jedi Purge. Is it too much to hope she doesn't become Face-Heel Turn fuel as the series progresses?
As for the season 5 finale she has left the Jedi Order, after getting zero support from her fellow Jedi (well, minus Anakin) when she was framed for a crime she didn't comit. Star Wars Rebels reveals that she survived past the events of Episode III and took on the identity of rebel cell leader Fulcrum.
The Clone Wars also revealed Darth Maul to be Not Quite Dead. The last we see of him he's being tortured by Sidious, who says he won't kill him and that he has plans for him. What happens to him after this is never addressed.
Though now Disney has nearly full rights and has announced Episode 7, so we may get some closure on those points
In the first of the 2003 Strawberry ShortcakeDirect-to-Video specials, Strawberry's pet Pupcake accidentally bumps into an arrow sign, making it point the other way. Although Strawberry sees this, she doesn't bother to fix the sign, which indicates that it should be a plot point later on. Yet the sign is never seen or mentioned again.
In the season three episode "Rainforest Schmainforest" (the one with the South Park kids being forced to join the Getting Gay With Kids Choir for an upcoming benefit concert in Costa Rica), Cartman keeps mentioning throughout Act I that Kyle has no dance rhythm because he's Jewish and, at the end of Act I, Kyle realizes this to his horror after Stan agrees with Cartman. With the exception of the bit where the kids' choir teacher apologizes to the Freedom Fighter leader for Kyle's crummy dancing in Act II, the whole storyline about Kyle coming to terms with being a lousy dancer is never fleshed out or even alluded to for the rest of the episode. (He does still dance badly in the dance at the end).
The episode "Coon vs. Coon and Friends" was really bad about this. The two previous episodes featured Tony Hayward and Captain Hindsight playing significant roles, but they don't appear in the finale or are even mentioned. There were also interdimensional beings besides Cthluthu who appeared in the first episode but were simply forgotten.
Captain Hindsight removed his own powers in the previous episode. Not much of a reason for him to be around after that.
Tweek becomes the "new Kenny" (translation: fourth main character) for the second part of season six. At the start of the third part, the Boys were inexplicably back to 3, despite the fact that an entire episode was dedicated to removing the previous fourth friend (who is still the fourth most important character to this day) and finding a replacement. Not only that, but Tweek is reduced to a Living Prop by the end of the season, made even weirder by the fact that some of the tertiary boys (or one-off in the case of Jimmy) became secondary characters afterwards.
"The Poor Kid" begins with Kenny and his rarely-seen siblings, Kevin and Karen, being taken into foster care. We follow Kenny and Karen throughout the rest of the episode, but Kevin disappears—they don't even throw in a line about him going to a different foster home or anything.
The episode "The Snuke" is a parody of 24 where Cartman believes that some Muslim neighbors are terrorists, and his quest to prove them as such leads him discovering real terrorists who have planted a suitcase nuke inside Hilary Clinton (the titular "snuke"). When the rest of the government discovers it they send an expert to diffuse the bomb, but he is killed and the last we see of Hilary Clinton in the episode the bomb is still inside her with no resolution as to whether it was removed/disamred or not. Given how 24 was infamous for pulling this trope all the time, the use here was more than likely an intentional part of the parody.
At the end of "201" we never found out how they got rid of Mecha Streisand. The Super Best Friends distract her with a Neil Diamond duet and that's the last we see of her.
In the Phineas and Ferb episode "I, Brobot", Candace captures one of the Ferbots in a sack, and it then gets picked up by the garbage collectors behind her back. We never see what happens to that Ferbot afterwards. Also, we also don't see what happens to the Candroid after the episode.
When the boys set Oompa Loompa-like Ba-Dink-A-Dinks free, they promise to "lay waste to the surface dwellers." But it's a one-shot gag — so far, their plot thread hasn't been resolved. They've had a few minor background appearances in subsequent episodes, but... not knowing where they are can be pure horror.
In the episode "Run, Candace Run", the conflict is that Candace has made too many promises to her friends, family and boyfriend, and she has to accomplish multiple tasks in one day. One of those was apparently something involving her and Stacy on stage in a cow costume, however, Candace seemed to forget all about that, as we never see her do it and it is never addressed again.
In the season 4 finale of Winx ClubAisha decides to take the flower that was revived with the gift of life back to Andros as a memento of Nabu. What Aisha did with the flower or anything else she did on Andros has been left unkown.
Oh, and what happened to Icy's pet duck after season 1?
Diaspro disappears part way into season 3 after she said Bloom hadn't had the last of her. Beyond mentioning she was banished, her plot-line is dropped. She reappears in season 5 to help Sky, and except for Bloom being uncomfortable with her around, nothing is made of it.
The pixies weren't seen or mentioned even once in season five. They returned in season six, but Digit and Tune were replaced with Cherie and Caramel with no explanation provided.
Several King of the Hill episodes had Bobby meet a girl and presumably ended up going out with her at the end of the episode. The next episode has him single again with no mention of the girl ever again (except for one girl, who was referenced in another episode and Connie, who was already part of the main cast when they broke up).
Bill is also like this. In one episode he's dating Kahn's mother and mentions that he's still dating her in another one. Then, all of a sudden, he's single and lonely again. They dropped her because they decided they liked Bill as his lonely, pathetic self. Makes sense, but it would've been nice if they had actually provided an in-show explanation for her disappearance.
Kahn's Mom is another example, after her initial appearance, she is shown several times in the background at her son's house, but then sort of vanishes, and a passing reference implies she went back to Laos.
Several plot motivations were also forgotten during the course of an episode in the series. One such example was from "The Courtship of Joseph's Father", where Dale Gribble has Joseph attend Spencer Academy over Arlen High School due to the fact that he was a great football player. The sole reason for Joseph being able to attend Spencer Academy (playing for the varsity squad) was never discussed while he attended the school.
"Returning Japanese" had a subplot where Luanne, watching over Ladybird while the rest of the Hills were out in Japan, thinks that she had died and gets a new, identical bloodhound. However, upon attempting to transfer Ladybird's collar to the new bloodhound, she jumps up and Luanne soon gets confused as to which one was the original Ladybird. The closest thing this got to any resolution was Luanne walking both of the dogs (using color-coded collars) and thinking of using the excuse that she learned cloning. The other bloodhound is not mentioned in any later episodes.
In the season 12 episode "Untitled Blake McCormack Project," Joseph meets a new girl named Kate and starts to find her attractive, only to learn that she is his half-sister (though both, along with Dale, remain in the dark about John Redcorn being the father). At the end of the episode, Kate and her mother move in with John Redcorn, but neither make a subsequent appearance.
An early episode of The Fairly Oddparents established Trixie as a closet tomboy, apparently setting something up between her and Timmy. This is never mentioned again.
A relatively unimportant example in the Batman Beyond episode "Out of the Past" is at the beginning, when Terry and Bruce are watching Batman the Musical. The Stage Batman picks up Robin from the chair, and he gestures up toward the Bat-Signal. When the camera pans back down, the six villains are all on stage, and Batman is center, but Robin is nowhere to be seen.
From another episode, Derek Powers is betrayed by his manipulative son Paxton, with the unwitting help of Batman. At the end of the episode, Batman hints that Derek is not dead, and we are also led to believe that Paxton will serve as a villain for the remainder of the series, or at least in the next season, in a similar capacity that his father did. Derek is never seen again for the rest of the series, and Paxton only appears in cameos.
Blight pops up again in the tie-in comics, by now having degenerated so much he's forgotten his entire past life as Derek Powers. Batman and Stalker fight him, ending with Blight being killed by molten steel.
One episode of Batman: The Brave and the Bold has Batman hit with a ray that gives him a copy of Plastic Man's powers. By the end, the ray is destroyed and the villain who made it is petrified. So Batman still has the stretchy powers unless he removes the power some other way. So... is this the dawn of Plastic Batman? ...come on. This is Batman you're talking about. He always has a solution.
It's never explained how exactly the Phantasm is able to teleport from place to place.
Also, Phantasm Andrea disappears into the smoke with her target the Joker; their fates are left unknown to Batman. Later Andrea is seen on a boat leaving Gotham for good, but no mention of the Joker's fate is made whatsoever. Joker is shown to be very much alive in the rest of the series, with no explanation of his escape given. However, Joker is well known for usage of Never Found the Body, which is why the trope Joker Immunity exists. This was eventually explained in a comic.
In Kong: The Animated Series, no final fate for Tiger Lucy is given. In the final two episodes, every other enemy is defeated one way or another, but Tiger Lucy, the fourth of De La Porta's henchmen (who has the least screentime of the four) is never seen nor mentioned in the final episodes.
An early episode had Kim and Señor Senior Jr. finding out they were a perfect match through a matchmaking fad. The episode ended with Kim finding her locker full of flowers and an e-card from Junior saying he awaited seeing her again. This was never brought up again; no Stalker with a Crush storyline, no Foe Yay (well, none from Junior), nothing. It just disappeared.
Googie is one of several new love interests introduced in the Superstars 10 films (Snulu for Boo Boo, Desert Flower for Huck, etc) which originally they had planned to make a whole other set of Superstars 10 films with some sequels to the previous batch. But near all those got pushed to the way side in the Turner boyout, turning most of the characters to forever be lost mice.
When the show was changed in the 80s there was no mentioning of what happened to Fred, Daphne and Velma. when Daphne returned to the show her exit was worked into the new premise but not explicitly stated on the show (she had gotten a job as a reporter). When Fred and Velma returned briefly in 1984, it was disclosed that Fred became a mystery writer and Velma was an intern at NASA.
In Teen Titans, Kitten disappears after her encounter with Starfire in "Calling All Titans", despite the fact that Killer Moth and Fang both appear in the Climactic Battle Resurrection. Kitten does just seem to be your average Spoiled Brat, having a half-moth father and a boyfriend whose head was a giant spider aside; she probably doesn't have any real combat training.
And then there's Red X who was originally Robin in disguise, only for the costume to be stolen by a an unknown thief. After is final appearance being in "Revved Up" he is never seen again (not even during the final battle in "Calling All Titans"). We never find out who he was behind the mask or how he got the Red X costume.
Speaking of "Revved Up", after the race for Robin's special suitcase, he opens it for his friends just before the end of the episode(the content's of the suitcase remain a mystery to the audience).
In Justice League, Supergirl's clone Galatea didn't seem dead upon her final defeat, but no one sees her again, nor is she ever mentioned. Considering she had a burn mark through her stomach, she was twitching, and had a comatose look on her face, she might as well be dead.
In Barnyard, the story essentially revolves around Otis, his dad, and a pregnant Cow named Daisy; Daisy later gives birth at the end of the movie. Come the spinoff series, Back at the Barnyard, and both Daisy and her son are demoted to non-speaking background characters in early episodes. They're eventually never seen again, instead replaced with Abby.
Essentially every Pony in the pilot episode to My Little Pony didn't appear in the series spinoff; mainly Firefly, Ember, Twilight, and Applejack. They were major to the plot, saving everyone in Pony-Land from being turned into slaves, but they were never mentioned again. There were, however, comics in the UK where they did appear. Ironically, Firefly, Twilight and Applejack were the inspirations for three of My Little Pony: Friendship Is Magic's mane six (namely Rainbow Dash, Twilight Sparkle, and Applejack, who was the only one whose name was kept unchanged).
The American Dad! episode "Hurricane!" has news reporter Greg get sucked up into the sky by the titular hurricane. A later scene has his boyfriend asking people if they've seen him, but it's not revealed whether he survived or if the storm killed him. Seeing as how he appears in the following episodes, he has in fact survived.
At the end of The Critic's run (at least a couple of seasons), Jay, who up to that point hasn't had much luck with women, was in a steady relationship with a mature, decent, likable woman, and despite a few stumbles, they were hitting it off great. Then comes the short-lived internet adaptation, and she's completely gone with no explanation (along with his son and longtime boss).
In the first webisode, Jay mentions his "second divorce", implying that the relationship ended badly, but no details are given. Still nothing about his son or (now former) boss.
Sonic Sat AM is full of examples. The first season had at least one episode where Sally is searching for her father. In the second season, she finds him, but no attempt was made to connect it with the clues found in her previous searches. In another second-season episode, they alter the past to ensure that their nanny survives to the present day, and it's revealed at the end of the episode that she does — and is never seen again. (To be fair, she probably would have become a recurring character in the following season, which never got made.)
This was the case with the original airing of Rudolph the Red-Nosed Reindeer. After it aired, Rankin/Bass received a lot of letters from children asking whatever happened to the Misfit Toys, who weren't rescued and never mentioned again after their scene. In response, they created a new scene for the end credits that showed Santa rescuing the Misfit Toys and delivering them to children, which has been the version that aired ever since. On the other hand, this leaves Yukon Cornelius licking the end of his pick unexplained - to make room for the new scene, the punchline to the aforementioned build-up had to be cut. (He was hunting for a peppermint vein, in case you were curious.)
Street Fighter had plenty. To quote the annotation near the end of this video: "What will Cammy do next? Can Ryu and Ken stop Akuma from murdering fighters and stealing their chi? Can T. Hawk set aside his feelings to stop Satin Hammer's terrorist vendetta against those who wronged her? Will Warrior's World ever be saved and will Chun Li ever reunite with her lover? Can Fei Long end the Triad's grip on Hong Kong and rebuild his tarnished career? Will Guile ever regain his old life and will Blanka regain his humanity? And what happened to Vega and Balrog?"
In the SpongeBob SquarePants episode "Grandma's Kisses", SpongeBob's grandmother puts Patrick to sleep on her couch. When the couch is next shown, Patrick is gone.
Squilvia appeared in one episode and was never seen or mentioned again.
There's also Squidward's pet female snail Snellie who appeared in "The Great Snail Race", she hasn't been seen since.
Transformers Prime ends with the DTV movie Predacons Rising, resolving all but one major plot line: the final fate of the villainess Airachnid, who was last seen going vampire on a horde of Insecticons after they were all trapped on one of Cybertron's moons. This is especially jarring when the entire movie takes place on Cybertron, without a single break back to Earth.
Speaking of Earth, after having elected to stay there in the final episode to help the US Military with ultra-major threats, Ratchet returns to Cybertron, but we never learn if he goes back to Earth, or what the human companions may have been up to in the meantime, let alone how they'd react to Optimus' Heroic Sacrifice.
Shockwave is seen being attacked by a horde of zombie Predacons and is assumed to be dead. However he appears later, damaged but alive, to urge the Predacons to help the Autobots stop Unicron. He doesn't appear in the final battle and disappears for the rest of the movie.
The original The Transformers wasn't immune either. The last we see of the Decepticons' human collaborator Dr. Arkeville is him telling Starscream that the 'Con has to go back to Earth (from Cybertron) personally. Afterwards, Arkeville is never seen again.
Exactly what did happen to the evil spell after it was driven out of Rarity, since the Tome of Eldritch Lore was (presumably) destroyed? Assuming that breaking the spell didn't destroy it entirely, of course.
What of the transformed band, turned into background ponies we've seen before? Are there two Octavias out there, one of which doesn't know used to be a very different, very male pony?
Tirek's brother is mentioned a number of times, and depictions of him are shown in a storybook, but never makes an actual appearance. Unless Tartarus gives Tirek enhanced longevity, his brother should still be around. Though considering he went back to wherever he came from and there is no easy means of long-distance communication except between Spike and Celestia, they might just not have been able to find him.
Where did Owlowicious go after he flew away before Twilight started fighting Tirek? Did he go back to live in Twilight's castle or did he just fly away?