General Zod from Man of Steel: His coup was actually a GOOD idea, albeit a little late. Jor El actually got in the way, though Zod killing Jor El was too far. Zod wanted to save Krypton, and believed that Jor El's method was wrong, as, indeed, as it turns out, Jor El HAD given up on Krypton and the Kryptonian Empire.
Zod also seemed to want to work WITH Kal El/Superman rather than kill him, but Kal said he would have no part it of it, so Zod I believe tried to hold Kal and his girlfriend prisoner at first but they escaped and tried to stop him. Zod believed that terraforming earth was the only way to revive Krypton, and he had been bred his whole life to save Krypton. It was like a brainwashed society (everyone was born pre-programmed to fil a certain role in society. Jor El and Lara broke the law by having Kal the natural way, so that he could choose his own path). Zod even says when his hope of recreating Krypton is ruined "I was born to serve Krypton! You have taken my soul from me!" And also, at the end, Kal El (Superman) seems very sorry that he had to kill Zod.
I also feel sorry for most of the Spiderman villains (except Venom, and, to a lesser extent, Norman Osborne). I feel most sorry for Flint Marko/Sandman, Max Dilon/Electro, and Harry Osborne (Green Goblin). Electro though, I feel the most sorry for, because he was ignored most of his whole life, got betrayed by Oscorp, it seemed, in his mind, that his hero Spiderman had double crossed him, and then he got locked up and experimented on. What he did to the city of New York was bad, but his lines of "Now everyone will experience what it's like to live in my world: a world without mercy, a world without power." just made me feel sorry for the guy.
Also, I felt sorry for Laurence in The Princess and the Frog. He wouldn't have gone bad had not Prince Naveen so horribly mistreated him, and even after he goes bad, it's clear that Facilier is just using him as a pawn (He even says they'll offer to split their takings for the evil plan 40% Laurence, 60% Faciler).
Also, I feel a tiny bit sorry for Mother Gothel. Her plans mainly were to keep herself alive, and losing that flower would have literally been the death of her, so she kidnapped Rapunzel, and she only attacked Flynn Ryder because he was coming to help Rapunzel escape, which also would have led to the death of her. She actually was willing to let Rapunzel heal Flynn in exchange for Rapunzel going with her quietly.
Another possible sympathetic villain could be, depending on one crucial fact, Zira from Lion King II. It would depend if she knew that the hyenas were the actual ones to kill Scar or not. If she did know, she's pretty nasty, deceiving Kovu like that and all. If she didn't, then think what it must have looked like to her:
1.) Mufasa is dead and Simba is believed to be dead too (why nobody asked for Simba's body is a mystery). Scar became king.
2.) Years later, Simba suddenly comes back and actually CONFESSES to having a role in Mufasa's death.
3.) Simba suddenly attacks Scar and demands that Scar confess that he killed Mufasa.
4.) After the fight between Scar and Simba, if Zira didn't see the hyenas kill Scar, then it would appear to her that either Simba pushed Scar into the fire or else Scar died from the fall.
5.) Simba then banished Scar's supporters, including Zira.
So, from her perspective, it may appear that Simba had a role in his father's death, ran away, came back when he was older, forced Scar to make a false confession, than had Scar killed, stole the throne, and kicked out the supporters of Scar, the true king.
At the end, Zira even chooses her own death, rather than get help from her enemies. (Another thing that makes me feel sorry for her.)
Another sympathetic character in Lion King II was Zira's son, Nunca. He was practically ignored by Zira, who kept doting on Kovu. It was only after Nunca's accidental death that Zira appeared to care for Nunca.