Jason Todd was tortured to death by the Joker, and when he came back from the dead, he had to live his life knowing that his mentor doesn't feel like killing his killer.
Arthur Fleck was born to an alcoholic mother who let his father abuse him, in addition to having a condition that forced him to laugh at the wrong time. As an adult, he was abused and shunned by his environment with the exception of a few good people. Unlike most Jokers, Fleck didn't do anything to deserve it.
The novel version of Dennis Nedry was working for the novel version of John Hammond, who was a very bad boss, and sufferes both financially and mentally. He was also exploited by Dodgson, who was more than likely planning to kill him after getting the goods. He wasn't nearly as evil as the cinematic Nedry. He wanted to bring the goods and get back and fix everything. Except the dilophosaurus caught him first. It was even less pretty that in the movie.
The Nolanverse version of Two-Face used to be a genuinely good lawyer named Harvey Dent, who wanted the best for Gotham and was Joker's second arch-enemy, until Joker killed his girlfriend and burned half of his face and brain during a sadistic choice game. I admit trying to kill James Gordon's child was a bit messed-up, but other than that, Two-Face had some solid points. If you don't count Catwoman as a villain, than Two-Face is the only sympathetic Nolanverse villain.
The hunchback of "300 Spartans" (forgot how to spell his name) was borned deformed in Sparta and was shunned by the harsh society for most of his life. Xerses took a ride on his misery, and living his life knowing his betrayal left him in a fate worse than death.
Tyrion Lannister was born as a dwarf to Tywim Lannister and a mother who died shortly after his birth. Twyin basically hated him because he was born, blaming him at the death of his own mother. Growing up at Tywin couldn't be an enjoyable experience either way. Let's just say there's a good reason for why Tyrion is the most sympathetic "Game Of Thrones" villain.
