The infamous F.A.C.A.D.E. incident. Long story short, Terry Kavanagh introduced a new baddie named F.A.C.A.D.E., and a huge deal was made about who he really was under the mask (well, helmet). Unfortunately, "The Clone Saga" began right after F.A.C.A.D.E.'s debut storyline ended, so the mystery of his true identity has never been resolved. It's become sort of a Running Gag that whenever the character does appear or get mentioned, there's usually some sort of joke about his identity.
Near the end of Brian Michael Bendis' tenure at Marvel, he began dropping hints in his Spider-Man series and Generations that Miles Morales would be abandoning the Spider-Man name in order to step out of Peter Parker's shadow and create his own heroic identity. This, coupled with Cable commenting that Miles would have a future in espionage, led some to conclude that Miles would become a costumed spy of some kind (rumored to be named Spy-D, the same name he used in the Marvel's Spider-Man cartoon). This was dropped after Bendis' departure, with the subsequent Miles Morales series by Saladin Ahmed keeping the character in his role as Spider-Man and focusing more on street-level heroics than spy stuff.
Mary Jane Watson was victim to multiple aborted storylines in between 2013 and 2018. First, her storyline getting back with Peter hit the skids when Doc Ock took over his body in the Superior Spider-Man storyline. MJ started dating a fireman named Pedro and was eventually Put on a Bus at the end of the Superior story, with only a few cameo appearances. That storyline came to an end when MJ was moved over to the Iron Man books to become a supporting character there, with no mention of what happened with Pedro and an offhand comment that her old club had burned to the ground, necessitating her move to another city. After spending years as Tony Stark's girl Friday and working with him to start a new covert spy agency, *that* storyline came to an abrupt end once she was moved back to the Spider-Man titles to rekindle her romance with Peter, with another offhand comment about how she stopped working with Iron Man and "Things not working out."
Spin-off Comic Books
Ghost-Spider (2019) ended with Gwen Stacy of Earth-65 (i.e. Spider-Gwen) getting beat in a curb-stomp battle by her versions of Sue and Johnny Storm, and subsequently blackmailed and threatened to abandon her home dimension, forcing her to live in the main 616 universe for the foreseeable future. This was followed up shortly after by her issues of the King in BlackCrisis Crossover, which not only ended with Mary Jane-65 stranded on Earth-616 alongside Gwen, but also had the cliffhanger that she contains part of the Carnage symbiote inside her. Cue Spider-Gwen: Gwenverse, and both Gwen and MJ are shown back on Earth-65 with zero explanation of how they managed to return, how Gwen managed to beat the Storm Twins to regain her title as New York's protector, and barely a passing mention of Knull. (Oh, and if Bodega Bandit finally got out of the hospital.)
Both Marvel Action: Spider-Man titles were hit with this:
The original series ended its 12-issue run with hints of The Kingpin being the overarching Big Bad. However, its relaunch only lasted three issues and had the Shocker acting on his own, thus leaving his presence behind.
The Continuity Reboot ended with the revelation of Norman Osborn behind the villains running the school Peter attends and Carlie Cooper beginning a Start of Darkness after catching Robbie Robertson and Cindy Moon talking to Spidey.
Films
The Amazing Spider-Man Series: One of the many Sequel Hooks at the end of The Amazing Spider-Man involves Peter attempting to track down the man who shot Uncle Ben. In The Amazing Spider-Man 2, this plot thread is never even mentioned. Likely this was meant to be continued in a future film, however with the series now canned so Spider-Man can join the MCU, it'll never be resolved.
The Amazing Spider-Man: Initially, the film contained strong hints of Richard Parker messing with his son's DNA (a la Hulk) and that Dr. Connors was involved with the deaths of Peter's parents, while also being more of a loose-cannon scientist ("Ready to play God?"); these were kept intact for the trailers. Due to early negative feedback pertaining to the movie's original "Untold Story" marketing, these subplots were altered or dropped (along with that tagline), but elements still remained behind in the final cut, leading to a few red herrings and loose ends.
Some of this can be seen in the deleted scenes, as it's evident mostly the Connors stuff got cut. It's pretty watered down from what the early trailers hinted at, but we do have Connors philosophizing about evolution and revealing that Peter's father didn't trust him because he felt he was radical. There's also some stuff about Peter becoming more than his father would have ever dreamed.
Throughout the film, Connors is shown wearing a wedding band and he has a moment while looking into his bedroom mirror at his missing arm and the empty bed behind him. A deleted scene also shows he has a son, so it's left up to interpretation what happened to his wife.
An intentional example is Peter looking for Uncle Ben's killer, as he ends up learning that being a hero isn't about seeking revenge and so he stops searching in favor of stopping the Lizard and saving New York - basically fulfilling his "great responsibility".
The Amazing Spider-Man 2: It seems the arc from the first movie of Peter hunting Uncle Ben's killer has been dropped, despite it being a Sequel Hook last time.
Spider-Man 3: Even though this was a major problem that caused strain on Peter's life and his relationship with Mary Jane in the previous film, it is never explained or shown how Peter managed to balance his life as a civilian and his life as Spider-Man, as his daily schedule in this film is exactly like his daily schedule in the previous film.
Venom: It's brought up that Venom is killing Eddie, causing his heart to shrink and multiple organ failures. This proves to be the entire reason why Anne separates Eddie and Venom. After that, it's not brought up again until the final scene. Venom does assure Eddie he can "fix it", but this comes across more as desperate pleas to not be separated from his host and it's not entirely clear if he actually can (And why he hadn't done so already if he could). The final scene of the movie does have Venom admit that Eddie's "liver is gonna start looking real delicious" if Eddie doesn't eat soon, suggesting that the repeated consumption of living flesh can stave this off and that Eddie was simply not adjusted to the Symbiote/eating enough yet.
Western Animation
Spider-Man: The Animated Series: The last season introduced elements that indicated they were going to develop The Clone Saga with a cloning scientist getting a sample of Spider-Man's blood. The plot of the Grand Finale even included took this story in The Multiverse as another incarnation of Spider-Man (fused with the Carnage Symbiote) having an identity crisis from his universe's Clone Saga and trying to go Omnicidal Maniac.
Ultimate Spider-Man: When the Lizard first appeared, a serum for scorpion mutations were seen as well. When the Scorpion finally appeared on the show, it was as as Badass Normal and later with a suit of Powered Armor. At no point did he ingest or get his powers from the serum.
Man-Wolf aka John Jameson. He only appeared once, still having the wolf's curse by the end of the episode. He is never seen again.
During the season one finale, Harry Osborn swore he would "get to the bottom" of what happened between his dad and Spider-Man, and have his revenge, suggesting he would become a new villain later on. But as season two rolled around, he showed no signs of actually investigating what happened to Norman, or of taking revenge on Spidey, instead settling on hating the webslinger from afar.
Near the beginning of Season 3, it was established that Echo, Gravity, and Speedball were potential S.H.I.E.L.D. recruits handpicked by Nick Fury to undergo training. One season later, we never see these three superheroes again.
In "The Parent Trap", Luke is exposed to a burst of energy when Scorpio suffers Phlebotinum Overload from a tampered batch of super soldier serum. At the end of the episode, his eyes glow with the same energy, suggesting that he would gain some kind of Mid-Season Upgrade. However, nothing ever came of this.
, and a huge deal was made about who he really was under the mask (well, helmet). Unfortunately, "The Clone Saga" began right after F.A.C.A.D.E.'s debut storyline ended, so the mystery of his true identity has never been resolved. It's become sort of a Running Gag that whenever the character does appear or get mentioned, there's usually some sort of joke about his identity.