Villain Has a Point

Time and time again a story is told with the classic hero vs. villain setup with the villain committing acts deemed evil by good, neutral, and the normally apathetic. The villain usually commits said acts for their own personal reasons. But wait, they have a justified reason for their actions? They may not be so much evil as they are anti. He may end up sending the hero into a depression after his motives come to light? Here my friends is a villain who actually has a justified reason for being what he is. Due to the nature of their villainy if they become too excessive in their methods it may fall under Straw Man Has a Point and they can easily fall under as a Well Intentioned Extremist. In-universe they can also easily fall under Designated Villain. Compare Anti Villain.

Anime and Manga

 * Yu-Gi-Oh Ze Xal has this with Kaito Tenjo. He believes the Numbers' cards are evil and from what has been seen the Numbers can easily make the good bad, (Ukyo, Fuya to a lesser extent) and the bad worse, (Jin, Rikuo, Kaio). Also, his claim that the Numbers want to destroy the world seems plausible seeing the evil from Black Mist who was able to capture Astral and control Yuma's body against his will. In fact, the only issue with him capturing Numbers is that he takes the soul of the person who possessed it.

Literature

 * In Isaac Asimov's story "The Dead Past", the government agents trying to prevent the protagonists from learning the secret of viewing the past seem like a classic heavy-handed Government Conspiracy... until it turns out that they're simply trying to prevent privacy from being utterly destroyed by the dissemination of devices that can view any place at any past time from a century ago to a microsecond ago.

Video Games

 * Dr. M from Sly 3 may be a terrible person to work with, a lab nut, and an overall Ineffectual Sympathetic Villain but he DID buy the island legally so everything is technically his and he could've claimed his right to kill Sly seeing that Sly invaded his land.

Western Animation

 * Justice League Unlimited: Project Cadmus created several threats to the world, but they do have considerable ground to stand on for their actions: the League didn't tell anyone about their big Kill Sat, they themselves have made questionable decisions in the past, and the Justice Lords were able to take over their world with only six of the founding members.
 * Also, Lock-Up, for nearly the same reason. It's telling that, when he shows up in the comics, Batman does briefly team up with him.
 * One from Batman Under the Red Hood. Under the Red Hood gives us one from the titular character himself. No matter how many times Joker may get slammed into Arkham, being the Cardboard Prison it is, he always returns at some point wreak more havoc. While Batman does think about killing Joker, he fears about never coming back. However among Batman's rogues gallery, Joker DOES have a higher kill count alone than most and will most likely never stop killing as long as he is able, so putting him behind bars or a padded room does no good. Yet because he's Batman he won't take that step. Some people find it easy to side with Red Hood here even though he is a bit demented.
 * The Equalists in The Legend of Korra claims that benders are forcing non-benders to live as second class citizens. Although it is not entirely true but they do show that there are bending gangs who abuse their powers to intimidate non-bending people and the city's council is solely consist of benders.
 * They get quite a bit of ammunition in the eigth episode when the City Council starts to oppress non-benders, arresting them simply out of suspicision or ANY association with members of the Equalists (this includes being a family member ). And it gets worse after we think a little bit. Later on in that episode we see what appears to be a whole neighborhood of non-benders.