One episode of Animaniacs found the Warner siblings transported to the deck of The Pequod facing Captain Ahab, shortly before the whale showed up. Ahab managed to survive this time (but he wasSwallowed Whole by Moby Dick, and as an added Mythology Gag, met Pinocchio inside its stomach).
Greta Attenbaum was killed by tomatoes in the original 1978 Attack of the Killer Tomatoes! film, but Mary Jo Nagamininashy, her corresponding character in the 90's animated series, remains alive and well throughout the series' run.
The series did an adaptation of the Secret Invasion story arc, where one of the most famous moments was Skrull leader Queen Veranke getting shot in the head by Norman Osborn, thus leading to Osborn's rise to power. Here however, she is merely neutralized at the end of the invasion and taken to custody in 42. The Wasp also notably lives in the Secret Invasion adaptation; in the comic storyline she was killed off at the end and stayed deceased for a long time.
The Falcon's mother is stated to be alive in Avengers, Assemble! (she even bakes cookies for the team, and appears in the episode "One Little Thing"), as opposed to the comics, where both she and her husband died when Sam was a child.
The Batman: The Animated Series episode ''The Laughing Fish" loosely adapts a 2-part comic story of the same name. In it, The Joker infects two random victims with a lethal dose of his joker venom. In the TAS version, since broadcasting standards wouldn't allow the writers to kill someone in a children's cartoon; instead, Batman is successfully able to administer an antidote to the venom after both get infected. Doesn't stop the scene from being any less freaky though.
The second Firestorm's origin had Ronnie Raymond dying in an explosion with his energies being inherited by Jason Rusch. The revised origin from this series spared Ronnie by making the second Firestorm the first one and having Ronnie share the Firestorm Matrix with Jason in place of Martin Stein.
Aquaman's son (see Justice League below). In the comics he was murdered as a child; in this continuity he's alive and well as a snarky teenager.
Princess Laethwen and the other Katarthans in the episode "Sword of the Atom", who died in their first comic book appearance when Ray Palmer accidentally destroyed their village while returning to normal size.
In Arkham Asylum: Living Hell, Junkyard Dog is killed by Doodlebug as part of a plot to unleash demons onto Arkham. In Beware the Batman Junkyard Dog is still alive, in part due to this version of Daedalus Boch being content being a petty vandal.
Queen Iolande's brother Ragnar was a minor villain in the Green Lantern comics, and was executed at the end of his first appearance for murdering a Green Lantern in an insane attempt to get his ring. In Green Lantern: The Animated Series, Iolande spares him and merely has him imprisoned, allowing him to return in a later episode as a Red Lantern.
In Warren Ellis' Iron Man: Extremis, Mallen is decapitated by Tony at the end of the story. The Iron Man: Armored Adventures adaptation of the arc changes the ending so that Mallen is simply taken into custody by Nick Fury. Far more notable examples of characters remaining alive in the series when they died in the comics would be Howard Stark and Obadiah Stane.
Ivanhoe: The King's Knight features neither Brian de Bois-Guilbert nor Reginald Front-de-Boeuf dying. Other animated adaptations feature only Front-de-Boeuf dying.
Aquababy in Justice League. In Aquaman's first appearance he sacrifices a hand to save his infant son from being killed by Ocean Master. In the comics, Aquababy was killed by Black Manta.
Subverted with Methuselah in the animated adaptation of Redwall. He appears to survive being injured by Chickenhound, only to pass away a few days later.
The first RoboCop cartoon showed Clarence Boddicker still alive and well despite RoboCop (1987) showing Boddicker getting killed by Murphy.
If the "King Homer" segment of the "Treehouse of Horror III" episode of The Simpsons can be considered an adaptation of King Kong (1933) (most would consider it an Affectionate Parody) then the giant ape survives. (But as Mr. Burns says, his career likely won't.)
In the Sonic Sat AM episode "Game Guys", Ari gets sucked into The Void. In Sonic: Friend or Foe?, a book based on that episode, he escapes with Sonic.
Ultimately subverted when Ari escapes from The Void in a later episode.
Emily Osborn is also alive and well; in the comics, she died when Harry was a baby. At the time, anyway; Marvel Legacy saw a character named Emma who became the nanny for Normie and Stanley, and Go Down Swinging reveals that "Emma" was really Emily and she'd faked her death upon realizing what kind of person Norman truly was.
Sally Avril as well. well as she died while Peter was still in high school.
Joan Jameson is also alive and well, despite dying in the comics well before Peter became Spider-Man.
Fredrick Foswell is also still alive and well by the end of the series, as opposed to his comic counterpart who died saving Jonah from the Kingpin.
Thunderbird was killed off in the X-Men comics after only three issues, but was still shown alive and well in the cartoon. This is due to the episode being a Backdoor Pilot for an aborted X-Men cartoon where he would've been one of the main characters. Presumably, this was for the sake of diversity, since the only other non-white X-Man at the time was Storm.
Sunfire's uncle as well. Sunfire killed him at the end of his first appearance in the comics, but the show ended with him hospitalized instead.
Terra was turned to stone, not crushed to death as in the "The Judas Contract" comic story. Cyborg mentions that it may even be possible to reverse her condition. The last episode implies this may have happened through unknown means.
Beast Boy in the comics joined the Titans after his original team, the Doom Patrol, died fighting the Brotherhood of Evil. In the cartoon, the Doom Patrol is alive and well, and Beast Boy simply left by choice.
Shredder in the Mirage comic was killed right in the first issue, resurrected once, then killed again. All animated adaptations give him Joker Immunity.
In the comics, Triceraton Leader Zanramon was (apparently) accidentally killed by his own men as they tried to rescue him from the turtles, who were holding Zanramon hostage. When the second cartoon adapted this story, however, they manage to recover him alive, and Zanramon was left free to plague the turtles a second time. Curiously, however, after the cartoon aired its adaptation, the still-ongoing comic retconned Zanramon's death again, revealing that he had apparently not died at all!
In the original comics, Splinter was the pet rat of dead ninja master Hamato Yoshi; in the first and third cartoons, Splinter is Hamato Yoshi. (The IDW comics came up with a creative way to split the difference: Hamato Yoshi died and was reincarnated as Splinter.)
The Rat King died after his first fight with the Turtles, and Splinter comes across his dead body in the comic books. Most adaptations prefer to keep the character around alive and well.
The villains in the Broken Ear episode of the Tintin animated series.
In the original Voltron Sven gets incapitated early on and sent for recovery. In Voltron: Legendary Defender, his counterpart Shiro stays on as The Leader of the Paladins. He does have a close call in the finale of the first season and season 2 ends with his disappearance, but both times he comes back anyway. Still, both fates are better than what happened to their collective GoLion counterpart Takashi, who dies in the battle Sven barely survived and is replaced by a Backup Twin later in the series.
W.I.T.C.H. has Yan Lin, Will's dormouse, Halinor, Cassidy and Nerissa either still alive or (in Cassidy's case) resurrected by the end of the series.
The entire nation of Genosha in Wolverine and the X-Men. In Grant Morrison's New X-Men run, the whole island was destroyed by a Sentinel invasion, leaving only a handful of survivors. The attack is far less severe in the cartoon, with no onscreen fatalities.
The show did an adaptation of The Dark Phoenix Saga. One of the most enduring, powerful moments in the original comic-book Dark Phoenix saga was when the Phoenix has a Heroic Sacrifice. In the animated adaptation, she died, but the rest of the X-Men were allowed to bring her back to life by each sacrificing a small part of their life force. It was like instead of Jean dying, everybody else had a head cold for a week or two.
Proteus was killed by Colossus in the original comics, but in the show, he gets a happy ending where he returns to his human form and reconciles with his parents. Ditto for his victims, thanks to the censors. In the comics, possession by Proteus was fatal, but in the show, it only resulted in extreme fatigue.
Bolivar Trask still pulls a Heroic Sacrifice in an attempt to destroy Master Mold, but unlike his comic book counterpart, he survives. (Unfortunately, similar to his counterpart, it doesn't stop the Sentinels from returning.)
Zatara... technically. He is now Dr. Fate's host. However, in the show, the Helmet of Fate contains the Lord of Order known as Nabu, and Nabu has a much less equitable relationship with his host than in most continuities, keeping absolute 24/7 control as surely as any villainous Puppeteer Parasite might. Zatara isn't dead, but he's gone forever just as surely and Zatanna mourns for him. It comes off as crueler than any actual death in the series (and it has a few.)
In Brightest Day, it is shown that Aqualad's birth mother died after being experimented upon by rogue Atlanteans. The show's tie-in comic reveals that his mother is still alive in this continuity.
Harm as well. He was shot dead by his own father in his debut story, but was simply captured by Zatanna and Artemis in the show.
In The White Seal, the seals herded together by the Aleut are clubbed to death. In the Chuck Jones adaptation, Kotik is able to scare the men away before they can start clubbing the seals.
In Finn Family Moomintroll, the giant fish known as the Mameluke is caught, cooked and eaten by the Moomins. In the Moominvalley episode based on this, the fishing trip is entirely unsuccessful and the Mameluke survives (or would have done if it existed and Moominpapa's story of how they nearly caught it was even slightly true).