Laeil Burbank goes out with a fairly tragic death, accented by how violently and sadistically she received her fatal injury and how she was almost saved. Found here.
Clio Gabriella gets a fairly touching send-off, dying in her boyfriend's arms while she begs for him to save her after being shot. Again, readable here.
In the Global Guardians PBEM Universe, the villain Hardcase was generally thought of as a brutish, selfish thug who liked to beat up women for fun, drank too much, and was generally a sleaze. And on September 11, 2001, he gave his life by using his superhuman strength to save people from the collapsing North Tower of the World Trade Center. The heroes not only campaigned to get him a posthumous presidential pardon, they sprang for a funeral the likes of which are normally reserved for deceased presidents and popes.
CT in Red vs. Blue (no, not the one from Season 7, the real Freelancer who the Rebel Leader took the identity of) was never really a villain in the first place, but instead ended up becoming a Hero Antagonist to try and take down the Director. Her reward for trying to do the right thing? A throwing axe to the chest which mortally wounds her, causing her to die in her lover's arms.
The Director also got a moment like this in the finale of Season 10, when he realised he should have spent more time looking after his daughter Carolina, realises that he has been chasing at ghosts futilely for several years, asks Carolina for a pistol, makes peace with her and F.I.L.L.S and then is implied to commit suicide.
Scion of Worm was unquestionably a sadistic, Omnicidal Maniac, but the way that Taylor defeated him by taunting him with the death of his counterpart makes it hard not to pity him.
Although a lot of the villains in Arby 'n' the Chief are usually downright over-the-top like Craig, or downright hateful like Adam, the series's final villain, Eugene Black is certainly an interesting case of this. As evident throughout the show's final season, he's a downright sadist who has no trouble letting his psychopathic or pedophile friends do as they wish to people online, as well as enjoys forcing hundreds of innocent people to replace their Xbox 360s after banning them with a hardware corrupting software over a period of 2 months, just for laughs. On the flipside though, he's also a failing student at his school (despite also being a bully too), is constantly abused by his Drunk (and sometimes neglectful) Father, and his sister (the only source of happiness in his life) is dying a slow and agonizing death of Leukemia. It's hard whether to feel sorry for him for how crappy his life is, or to hate him for how much of a bastard he is just to repress these feelings. To add insult to injury, this only get worse for him, and he's Driven to Suicide by the show's end.
Ask That Guy with the Glasses goes out with a strange mix of this and Death as Comedy. In the Grand Finale, someone asks him "do you have a question?". He gets so excited that someone finally thought about what he wanted that he literally explodes. Lampshaded by Chester A. Bum, who is sad when he first finds out about That Guy's death, but then realizes that he was a terrible person and it's probably a good thing he's gone.
Critical Role has one with Delilah Briarwood. She and her husband Sylas are, by all accounts, a loving couple who care for one another very, very deeply. They are also truly terrible people, and are the ones responsible for the massacre of protagonist Percy's family and household and the trauma he endured as a result, as well as unknown other evils. But even after the horrible things they did, critters and players felt bad for Delilah, due to her absolutely heartbroken reaction when she saw Sylas killed right before her eyes.
Marble Hornets: The two main antagonists of the series, Alex and Brian, both die with some degree of sympathy. Alex practically begs Tim to finish what he started, implying that while he may have gone Ax-Crazy, he nonetheless believed that what he was doing was right. Brian, on the other hand, is revealed to be the Hooded Man shortly after his own demise. Seeing the sharp contrast between his personalities before and after encountering the Operator makes the viewer sympathize with him as well.
At the end of The Suffering Game, Lydia dies of despair when Edward is killed; in her final moments, she drops her illusory form in favor of her true black robes, and, at a loss for words, simply screams.
John might be the source and avatar of the Hunger, but watching him get subsumed by it is more than a little tragic. His actual death, watching the sunset with Merle before fading away, only makes him more sympathetic.