Major Jakov. The sheer brutality with which Barry usurps and then murders him makes his death a dramatic moment, both for the audience and In-Universe.
If he even counted as a villain, then Captain Murphy-he wasn't even a bad guy, just a harmless, if unstable, guy who went nuts and started making terrorist threats due to being trapped at the bottom of the ocean, but Archer's idiocy gets him killed, and he tells them how to escape the lab with his dying breath.
In Beast Wars, although it's fairly minor, Dinobot does seem to briefly mourn the untimely deaths of the Predacons in victory. Whether he still feels a sense of affection and camaraderie for his former teammates (as Optimus assumes), it's more likely he saw it as a waste of warriors who deserved honorable deaths. He even quotes William Shakespeare!
Alas, poor Tarantulus! I new him, Cheetor! This is the leg that stalked so many victims! (Sighs) So it should come to this...
In Beast Machines, Rhinox, a former ally, has become Tankor, a powerful enemy. After Tankor's death, the heroes hold a memorial for their fallen friend.
Cheetor: He wasn't just one of us... He was the best of us.
Beetlejuice: Claire Brewster can be considered villainous, with her massive ego and strive to humiliate Lydia (she'd succeed if not for the Ghost With The Most). But one episode had her rung through the wringer on a Beetlejuice-staged foreign exchange student program to where she's dirty, dishelved and her clothes are torn. When she tries to enter her own home for a big fancy party, the butler dismisses her as a poverty-stricken waif. Lydia (at the party) sees Claire outside crying her eyes out, so she sneaks Claire in through a back window, cleans her up and gets her ready for the party.
Vlad Masters in Danny Phantom, the Big Bad of the show, and performs his share of evil acts. Still, in his final moments he not only had to deal with the fact that everyone he wanted would not give him their love, but his most hated "friend" of all people rejected him when he refused to change his evil ways. Now, Vlad doesn't have anyone and is stuck in an area where he has to confront his greatest fear: loneliness.
In nearly every Mr. Freeze appearance (except the one where he finally gets a happy ending and the one from The New Batman Adventures), he is defeated in a tragic and Tear Jerky way, culminating in this final exchange in his last appearance (both in Real Life and in the Universe timeline), where he lets himself be caught in a collapsing building.
Batman (Terry): You gotta get out of here, Freeze! The whole place is gonna go! Freeze: Believe me... you're the only one who cares.
Solomon Grundy in a single episode (or rather two connected ones), goes from regular villain to sympathetic villain, who dies in his quest to attain his lost soul. For good measure, he's brought back again in a later episode, this time truly soulless, and has to be put down Old Yeller style.
Grundy: Do you think... Grundy's soul is waiting for him? Hawkgirl (An avowed anti-theist): Grundy, I don't belie- (stops herself) Yes.It's waiting for you. Grundy: Then Grundy... gets his reward.
General Shiva in Exo Squad; imprisoned for not slaughtering the Australian Resistance to the last man, he is given a chance to "redeem himself" by retaking Venus, which he knows to be a suicide mission. But, being a good soldier, he gives it a go anyways. When he gets shot down, even the Exoscouts who find him see it as a tragedy.
Played for laughs in the Futurama episode "Anthology of Interest I". In a fantasy sequence, Bender is depicted as a giant who smashes up a city before being killed. As he lays dying, he laments he was unable to carry out his dream of killing all humans and expires on this line:
Bender: "Who's the real seven billion ton robot monster here? Not I. Not... I."
Gargoyles has the Captain of the Wyvern Castle guard, who was so wracked with guilt for accidentally causing most of the Gargoyles' deaths when he betrayed Wyvern Castle to the Vikings that he spent the next thousand years haunting the castle's remains after his death.note Hakon was supposed to spare the gargoyles, but he didn't keep his part of the deal. Hakon was also haunting the site, but out of continued hate for Goliath (who ironically had nothing to do with either of their deaths who killed each other Disney style, although he wanted to deliver a gruesome kill). When Goliath shows up at the castle again, they harass him, make him hallucinate and attack his own friends, and, finally, drive him to an ancient ritual site where they can exchange his life for theirs. The Captain realizes what evil he is about to commit, repents, and uses his brief physical form to destroy the site. With his last moments, he thanks Goliath for forcing him to acknowledge his sins and begs for forgiveness as he travels to the afterlife. Goliath happily mourns him as a friend who is finally at peace. Hakon is still stuck, trapped within the ruined site, alone to wallow in his hate.
In The Legend of Korra, Tarrlok and Amon/Noatak end up on a boat escaping Republic City after Noatak's lies are revealed to the public. Deciding they could not live, for any various amounts of implied, but unsaid reasons (being the legacy of an evil bloodbending criminal, knowing they'll be hunted for the rest of their lives, coming to terms with evil deeds), Tarrlok uses an Equalist shock glove to blow up the boat's engine, killing both of them. This follows Noatak having said he wanted to start a new life with his brother. Tarrlok even remarks "it will be just like the good old days," and Noatak remarks how he almost forgot the sound of his own name and sheds shed a single tear right before the explosion. Depending on who you ask, the tear indicates (among other interpretations) that he knew what Tarrlok was about to do and didn't try to stop him, or that he genuinely wanted to have the peaceful life with his brother that he'd been talking about.
It's very hard not to feel sorry for the Villain Protagonist of the "The Tale of X9" episode , a robotic assassin, who was one of several murderous robots created by Aku, but was the only one given emotions and feelings. After years in the service of Aku all the other robots of his series have been destroyed, but he has survived because of his emotions. However, when he meets a tiny dog named Lulu (sweet thing), he finally hangs up his assassin hat for good. Unfortunately, when Jack arrives, Aku becomes desperate and decides that he has to pull his greatest assassin out of retirement by holding Lulu hostage. Jack knows nothing of this, and when X9 launches his attack, Jack cuts him down just as effortlessly as he would any other mook. His final words are asking Jack to finish caring for his now abandoned charge.
Princess Mira from "The Princess and the Bounty Hunters" is another enemy of Jack's that is after him for a noble cause; she hopes to use him as a bargaining chip to free her nation from Aku's tyranny. When she and her allies ambush Jack, he effortlessly dispatches all of them with only Mira standing. Realizing that she is so badly outclassed by the samurai, Mira can only slump over and cry, seemingly accepting that she will never save her people, while Jack wanders off into the forest without a word.
In Season 5, Jack is pursued by female assassins known as the Daughters of Aku, whom were brutally trained from birth by their abusive mother with the purpose of killing the samurai. While Jack himself is initially unaware of this, its made abundantly clear to the viewer that they were just abused young women than anything else. When he is forced to kill one in self-defense, its treated as a very somber moment for marking the first time he killed a real human being and not a robot. And after killing five more in combat, Jack is so wracked with guilt he begins to hallucinate with dozens of crows calling him "MURDERER".
Savage Opress from Star Wars: The Clone Wars caused more than his share of death and destruction while apprenticed to Count Dooku, Asajj Ventress, and later Darth Maul. However, this was due in large part to his brainwashing at the hands of the Nightsisters, and when he is unceremoniously impaled on the lightsabers of Darth Sidious, he dies in his brother Maul's arms, expressing regret that he had not reached Maul's expectations.
In Star Wars Rebels, the death of Darth Maul is a major Tear Jerker, one of the biggest in the whole series, when he realizes how badly he's failed and how much of his life has been completely wasted. He's past his prime, everything he has worked for is for nothing, his family is dead, and he spends his time tracking down Obi-Wan Kenobi for one more duel. As Maul dies, the two have a quiet conversation on the Chosen One and Maul saying that he will avenge "us" - Maul, and either his brother or Obi-Wan.
Also from Rebels, there's Imperial Lieutenant Yogar Lyste. Despite being a jerkass who seized land from innocent farmers for the Empire, it's hard not to feel sorry for him when he gets framed for treason by the actual Reverse Mole. He's last seen being dragged away protesting his innocence, and the only person who actually seems to care about what happens to him is the same man who framed him in the first place.
Jasper from Steven Universe. Before being corrupted, she's revealed to be an angry and vengeful loyal soldier who, from her point of view, lost her colony, her planet and her leader (Pink Diamond) because of Rose Quartz. She spends her last moments roaring at Steven for every wrong she thinks Rose Quartz did. On top of this, it's implied she's nothing more than the equivalent of a grown up Child Soldier who's been indoctrinated from birth to think the way she does. Word of God later confirmed that she refused Steven's help because she hated herself for being (in her eyes) too weak.
Bismuth is also this. Fighting in the war against Homeworld, she saw her comrades shattered at the hands of Homeworld Gems. She believed they'd lose the war unless they stopped following Rose Quartz's policy of not shattering enemy Gems. When she made a weapon designed to do just that, Rose was mortified. She poofed Bismuth to keep her from telling the others, and lied to her friends about her disappearance for 5000 years.When Bismuth is stabbed with Rose's sword by Steven, she delivers some heart-wrenching words before she poofs.
Bismuth: You should have shattered me back then. At least if I were in pieces, I wouldn't have to know how little I mattered to you! You didn't even tell 'em. You bubbled me away and didn't ever tell your friends. My friends! Steven: I'm going to tell them. I'm going to tell them everything. Bismuth: *chuckles* Then you really are better than her.
The Rubies are a generally incompetent, childlike morons, aside from Eyeball, who has a little more experience due to being a Shell-Shocked Veteran. All of them are Thrown Out the Airlock by Steven, a possible Fate Worse than Death, due to the fact Gems don't need to breathe and are The Needless, condemning them to a possible eternity of floating through space, something Steven expresses heavy guilt over in later episodes, in addition to the fates of Jasper and Bismuth.
In the Teenage Mutant Ninja Turtles (2003) episode Nano, a colony of Nano Machines are separated from the main group, and create a body made from junk, which is found by a jewel thief who "adopts" it (seeing as it has the intelligence and personality of a child) and uses it to commit crimes. Eventually, as the nano-bots multiply and it gets stronger, the Turtles have to destroy it by dumping it in a vat of molten iron, but they're pretty bummed about it later:
Michelangelo: I kinda feel sorry for the guy. He was like a little kid.
Donatello: Too bad he had such a rotten father...
Hun in Turtles Forever, after the Turtles finally convince him that The Shredder is going to destroy The Multiverse. Hun is erased from reality right afterwards. The same thing happened to Casey and April; they both get better once reality is restored, Hun was likely brought back too.
Leonardo: You heard the man. Let's go stop the Shredder.
The Decepticons got some of their members killed unceremoniously. Breakdown was eviscerated by Airachnid. And Dreadwing, who wanted to kill Starscream who zombified his brother Skyquake, was killed by Megatron for disobeying his order to stand down.
Additionally, several MECH members end up being killed by Silas as he views them as useless now he is a human-Transformer hybrid, just after they saved him of all things. It's pretty hard not to feel sorry for them in this case.
TRON: Uprising: Keller's a scientist forcibly drafted into the occupation to force them to mind control other programs. She chafes, and helps the Renegade stop her concoction before going on the run, with the Occupation force chasing after her. She spends an entire episode in a state of panic, trying all manner of options to desperately escape while trapped on a train, nearly dying at least twice, and Beck, sympathetic to her position, trying to recruit her. At the very end, cornered, she goes back to the Occupation with Paige promising her no harm, but not before covering for Beck so no one knows he's a Resistance sympathizer. She goes to back to the general, who welcomes her back, and kills her like every other minion who displeases him.
Likely because, on top of everything else, Nox had managed to convince himself (and attempted to convince others) that it was okay to do any horrible thing in pursuit of his goals because it would all be undone when he finally succeeded. He'd get what he wanted and no one would really be hurt. But of course, it didn't work out that way.