In Adventure Time, Marceline's father, the Lord Of Evil, is sealed in the Nightosphere. Finn frees him, not knowing how evil he was. In the end, Finn manages to seal him back into the Nightosphere. Even worse is the Lich, the Ultimate Evil who was imprisoned inside amber within a great tree by the legendary hero Billy. He finally broke free during the season 2 finale.
In an episode of Alfred J. Kwak, Alfred encounters the Evil Spirit of Darkness, an ancient demon who caused so much torment and destruction that God locked him inside a magic bottle.
In Animaniacs, the Warner Brothers (and their sister Dot) were Sealed Zany in a Water Tower. In this case, it was more Sealed Chaos in a Can.
Beast Wars brought us Protoform X a.k.a. Rampage. He was the result of Maximal experiments to produce an immortal super-soldier by copying Starscream's mutant spark. They got that part right in the form of an unkillable serial killer that slaughtered human and cybertronian alike. After eventually capturing him, the Maximal Elders sealed in up in a stasis pod then turned him over to Optimus Primal's to dump on some desolate asteroid since they could figure out how to destroy him. Several adventures later and the monster was unleashed again and recruited by the Predacons.
Vilgax, from Ben 10, tends to be put in a can of whatever sort between appearances, be it a healing chamber, a block of ice, or a pocket dimension. He's slightly unusual in that we see him out of the can first.
And in the same show, Ghostfreak/Zs'Skayr is an odd example of evil that got sealed in a can accidentally, his DNA sampled for the show's Clingy MacGuffin so that the wearer can turn into him, and the personalities of his species being encoded in their genes somehow. Eventually, he gets loose and becomes Ben's Enemy Without.
Buzz Lightyear of Star Command had Natron the First in the aptly named episode "Ancient Evil". After he is defeated and returned to his tomb, Mira melts the door to it. Hopefully this will keep him sealed.
The Care Bears Movie had the Evil Spirit, whose can was a locked book of magic spells a young boy, Nicholas, opened. The spirit is powerful but, since it's confined to the book, needs Nicholas to cast its spells; he becomes progressively more evil in the process. The Power of Friendship helps him come to his senses and he helps close and relock the book, ending the threat.
ChalkZone had a two-part episode called "The Big Blow Up", which was about Rudy Tabootie opening the door to the temple of King Mumbo Jumbo and in doing so accidentally freeing a swarm of creatures known as Inflatermaus, who were imprisoned in there for centuries because their bite infects inhabitants of ChalkZone with a fatal disease called Balloonemia. Upon being freed, the Inflatermaus swarm begin to infect the people of ChalkZone again and it is up to Rudy, Penny, and Snap to find out how to cure Balloonemia and reimprison the Inflatermaus swarm before it is too late.
In the prequel episode of Code Lyoko, we discover that the dormant Supercomputer was sealing XANA for 10 years. It is Jérémie, by turning it back on, who unleashed the malevolent program (plus his future girlfriend) on the world.
Nicolai Technus spent a fair amount of episodes imprisoned in Level Zero of the Doomed video game.
Fright Knight was sealed away inside a pumpkin, and was released first by Danny himself (accidently), and later by Pariah Dark so that he could act as The Dragon.
Pariah Dark was sealed away to free the Ghost Zone from his tyranny.
Vlad seems particularly fond of releasing these - he released Pariah Dark unintentionally, and then later on intentionally releases Vortex on the world and then quickly loses control of him.
Any ghost trapped in the Fenton Thermos. Temporary, but still sealed away.
Technically not a can, but Pandora's box definitely qualifies.
The Ultimate Enemy: Dark Danny was sealed away in a Fenton Thermos and left with Clockwork, though for how long is unknown.
In Di-Gata Defenders the plot of the first season is for the titular Defenders to reseal an obscenely powerful entity known as the Megalith that the seasons' Big Bad used to take over most of the world a generation ago. However, the defenders decide on a change of tactics after finding out that not only has this thing been sealed and escaped numerous times in the past, but that it gets better at unsealing itself each time.
The Megalith happens to be keeping another evil sealed in another dimension.
Felidae's Claudandus means "something that must be sealed".
In The Flintstones, it can be argued The Great Gazoo was this to his people. He invented a death machine and they stuffed him in a satellite and sent him to Earth's stone age. Turns out in this case he's not such a bad guy, but it was a dangerous machine that got him sealed in his respective can.
In The Godzilla Power Hour, the Cyclops was so invulnerable that even the Sufficiently Advanced aliens who discovered it couldn't destroy it, so they trapped it on an island behind an impenetrable force field. The sucker's so tough, even Godzilla doesn't successfully destroy it at the end, so the crew just ends up trapping it back behind its force field.
In Gravity Falls, the wax statues in "Headhunters" were locked away for ten years before Soos stumbled across them and they were able to seek their revenge.
The Red Sentients in Hot Wheels Battle Force 5. They were sealed away in five seperate Battle Zones by Zemerick when he betrayed them. At the end of season 2, Krytus is freed by a traitor named Praxion (whom he promptly drops off a cliff) and proceeds to release the rest of his team from their own prisons. The rest of the Red Sentients were all frozen by Sage before they could join Krytus in his multiversal conquest. These are ultimately a subversion, as it turns out they're just as tired of the war as the Blue Sentients are when they're released and gladly make peace instead. They then reseal Krytus in a block of ice on a distant world as punishment.
All of the Inhumanoids were locked away for thousands of years before the beginning of the series. Tendril was chained up 2 miles underground, D'Compose was trapped in amber, Metlar held by a being with magnetic powers, and Sslither covered with concrete. And Blackthorne Shore freed all of them, the former three in the pilot alone.
Most seasons of Jackie Chan Adventures involved the cast attempting to reseal escaped Sealed Evil in a Can once using a jar-like object. In the series, this is justified by the fact that destroying evil will only allow a different (and probably stronger) evil to take its place. Better then to keep around the evil threat you already know how to deal with, than risk leaving the way open for something far worse to come up that you may not know how to deal with in time.
In other words, the devil you know is better than the one you don't.
In addition to the main villains, there was also Spring Heeled Jack, who was turned to stone long ago and accidentally released and the Monkey King, who's imprisoned as a puppet.
Hades, Greek God of the Underworld, in Justice League. Released by Felix Faust in the hopes that Hades will grant him "ultimate knowledge" in return. Hades naturally betrays Faust by causing him to instantly age to an old man since "Ultimately, pain and suffering are all humans will ever know."
Kim Possible had some sort of a sealed evil monkey man who petrified people in one episode. His name fit him perfectly, The Yono
Chiros, the secondary antagonist of Kong: The Animated Series. Imprisoned in a stone tablet that is implied, by Harpy cautioning the gargoyles moving it, would turn out bad for Chiros if it was broken (whether it will actually kill him or simply prevent him from being released ever again is unknown). It is also unknown why it was never destroyed the first time he was sealed inside it. At the end, Chiros is released, but Lua opens up a portal and Kong spins him by the tail and throws him back in, sealing him inside the tablet again. Kong immediately smashes the tablet.
The Legend of Korra: Vaatu, an evil spirit who is the embodiment of chaos, is sealed in a dead tree in a desert by the first Avatar, in the Spirit World; Vaatu's design is similar to Aku's, as is his prison (evil spirit sealed in a dead tree in a swamp), which is itself a reference to Hexxus (toxic spirit sealed in a dead tree in a dead forest).
The singing, dancing frog who ruined a man's life in the Looney Tunes short "One Froggy Evening" was placed into a cement slab and freed several hundred years in the future. The frog was also found by the man in question in that cement slab, so he may have been taken out of and put back into the slab many, many times by all the men whose lives he had ruined.
This is based on the story of a real (not evil) horned lizard that was sealed in the cornerstone of a courthouse (long before they were on any endangered species list). 31 years later the stone was opened and the horned lizard was alive and lived on for almost a year afterward.
In ˇMucha Lucha!: The Return of El Malefico, El Malefico was imprisoned in the core of the Earth for 100,000 years. He used The Flea to trick Rikochet into freeing him by reading a passage from the Code of Masked Wrestling backwards. At the end, El Malefico is defeated and he is sealed back up again.
Nightmare Moon was sealed in the Moon for a thousand years as "The Mare in the Moon".
Discord had been imprisoned in a stone statue by Celestia and Luna since ancient times for the suffering his rule brought everyone in Equestria. However, his prison weakened over time, and the Cutie Mark Crusaders release him by creating discord (fighting) in front of him, giving him the power to break free. The Mane Six put him back in his can at the end of the two-parter. Eventually, though, they release Discord and reform him when Celestia decides she has use for his powers.
"It's About Time" reveals that there are a bunch of evil creatures and villains sealed away in Tartarus that are guarded by Cerberus. In "Twilight'sKingdom", one of these villains manages to break out.
King Sombra was turned into a Living Shadow and imprisoned in the northern ice by Celestia and Luna. They were at least more thorough than with Discord.
In "Inspiration Manifestation", the tome was hidden away and locked behind a caged door for a reason. But Spike fails to notice any of this.
The mischievous spirit in "The Box Of Dirty Tricks", which is sealed inside a box in an attempt to contain it from doing anyone any harm. Not that it stops the spirit entirely from doing its dirty tricks upon whoever possesses it.
Mystico the goblin from "Nobody Smurf", who was sealed inside a fountain and was accidentally released by Nobody and Clumsy Smurf when they knocked over a goblet near the fountain that they were not supposed to touch.
The druids in a tree in the episode "The Smurfs' Time Capsule". Only their leader managed to escape so that he could get the Moonrock Amulet and free his brothers when the light of the full moon hits the amulet. The Smurfs stopped his attempt and sealed the druid leader back inside the tree.
The evil wizard trapped in the Swapping Well. (Papa Smurf was the one who had trapped him there, it turned out.)
The Mad Artist Maestro, who was trapped in a painting for making art that could do that to living creatures, inadvertently released by Painter Smurf (who Maestro affectionately called his "apprentice" later; Painter later had to create the most convincing work of his life - as he said - in order to put him back.)
In an episode of Sonic Sat AM, Robotnik steals a computer of magic spells from the formerly evil wizard Lazar, and Sonic attempts to get it back. When asked why he can't just destroy the computer, Lazar says that would release all the evil it contains.
In the SpongeBob SquarePants episode "Mermaid Man and Barnacle Boy III", the Mermaid Man and Barnacle Boy villain Man-Ray is shown to be imprisoned in frozen tartar sauce. SpongeBob and Patrick, who were watching over Mermaid Man and Barnacle Boy's headquarters in the superheroes' absence, end up accidentally thawing Man-Ray out. The villain escapes to resume wreaking havoc after tricking SpongeBob and Patrick into removing the tickle belt used to restrain him and exposing them to the Orb of Confusion, but he ends up doing a Heel-Face Turn after finding that the tickle belt's made him unable to commit crimes without bursting into laughter.
SWAT Kats: In the first episode, the Pastmaster is Sealed Evil in a Treasure Chest. We don't learn he exists until after he gets unsealed.
There's also the Mad Kat The Insane Jester, who was sealed in a jack in the box.
Trigon in season four of Teen Titans, where his daughter Raven becomes his portal into the world, allowing him to turn every creature in the biosphere into stone and cover the planet in lava.
Also, the dragon Malchior in an earlier episode qualifies, sealed in one of Raven's spellbooks.
In the Tiny Toon Adventures episode, "The Looney Beginning", when Buster and Babs need to find villains for their series, they find a box known as the "Villains Box", that has signs with warnings such as DANGER!STAY OUT! and GO AWAY! written on it. Upon opening the box, it releases many of the series' villains, many of which are minor and one-shot characters, such as the Candy Bar Monster from the "Best O' Plucky Duck Day" episode segment, "Sticky Feathers Duck", The Devil from the ending to "Sawdust and Toonsil", The Metropolis Marvels from "The Acme Bowl", and Dr. Gene Splicer from "Hare Raising Night". Eventually, it gets down to Dizzy Devil, Elmyra Duff, and of course, Montana Max.
Total Drama All-Stars: Mal, Mike's evil personality who was incarcerated in the same juvie Duncan was in sometime prior to the series. After he was pardoned from juvie Mike was able to take control and seal him in his mind, years later Scott accidentally hit him as Manitoba Smith in the head with a shovel, partially freeing him.
For 4 million years, the Ark held the Decepticons and Autobots in stasis, under a volcano... until volcanic activity shook things up and woke up the evil Decepticons.
In Cosmic Rust, there's a dead planet with radio beacons warning travelers to stay away or die horribly. The Decepticons plunder it, and in the process, catch the metal-eating plague called Cosmic Rust.
In Return of Optimus Prime, the Hate Plague spores were sealed inside a star after their last outbreak. Unfortunately, the star went nova.
Starscream himself could be considered Sealed Evil in a Can in the episode Starscream's Ghost; his ghost first appears after Octane tumbles into the Decepticon crypt and knocks over the ruins of Starscream's grave marker.
Deconstructed in Transformers Prime. After Unicron's defeat by Primus, his body was cast away into the depths of space. His gravitational pull attracted matter over billions of years which coallessed into the Earth itself. Unicron's physical form is the Earth's core, but he can control the mineral deposits on the surface and create golems of himself, among other things. Played straight when Optimus traps Unicron's Anti-Spark (his soul basically) inside an indestructible reliquary in the series Grand Finale.
Simon and Snarf in Trollz; while the Magic of the Five was sufficient to release Snarf, Simon had to trick the girls into helping him, as he could only be freed by someone pure of heart helping him of their own free will.
Valtor from Winx Club may count as sealed evil in a block of ice, until the Trix released him in the beginning of season three.
The position of Phobos and several of his most powerful minions for most of the second season of W.I.T.C.H. until he gets released by the heroines. Nerissa was also once a Sealed Evil In A Can, but she escaped several decades before the series begins.
Wuya from Xiaolin Showdown was trapped in a puzzle box for 1,500 years until Jack Spicer freed her unwittingly.
Likewise, Hannibal Roy Bean was trapped in the Yin-Yang world for nearly as long until Omi freed him unwittingly.
And then there's Sibini, who was trapped in the Mosaic Scale until "The Evil Within".
In an episode of SheZow, BrouHaHa was imprisoned in a vacuumn cleaner, that also happened to be in a box, by Anges Monroe, the previous SheZow. He was imprisoned there for 61 years, until some unwitting customer brought it off Guy Hamdon, the current SheZow, in a garage sale.