CAA: Christian Anime Alliance

What are some anime villains who, throughout a portion of the show or the whole thing, were very bad people who the audience would of thought had not an ounce of goodness in them but realize their mistakes and the wrong of their ways by the time of their death?

I've always quite enjoyed those sorts of scenes in animes.

I'm pretty early in the series, but it's looking like A Certain Magical Index might be doing this.

Basically every villain in Gintama has some sort of realization like this. It has a way of making a character look like scum and then making you care at least a little about them in the end. Can't think of any more right now but they'll come to me...

There's a great one at the end of the original Mobile Suit Gundam with Char. He's not super evil, but he's been fighting for Zeon, who are pretty much space Nazis, so that he can get revenge on the family who killed his father, twisted his father's ideals and took control of Zeon. Over time, he develops this rivalry with a hotshot kid pilot named Amuro on the opposite side of the war, and they clash at some of its biggest battles, and through other circumstances the battles become hugely personal. SPOILER: Highlight text to read: Eventually, though, the tide turns and Zeon starts losing, and losing badly. The last episode is giant robot D-Day in space, and Char and Amuro have this incredible fight; they end up trashing each others' mecha, but keep fighting on, literally wrestling with each other through the Zeon fortress. Then Char's sister shows up, tells him how foolish fighting with Amuro is when he could be fighting this ruling family behind it all; Char goes "Oh! Right!" and strikes the decisive blow, apparently sacrificing himself in the process. So it's redemption for the wrong reasons, but it counts, right? It's one of my favorite scenes in anime, definitely a great way to end the series.

The main one that's coming to mind for me is Scar from FMA. He's not the main villain, but he's a pretty dangerous adversary for much of the story, and in both the first anime and Brotherhood, he ends up going through a lot of character growth by the end.

Not technically an anime example, since this doesn't appear towards the end of the Visual Novel, but Beatrice from Umineko no naku koro ni is a great example of this.

At first you think she is nothing more than an incredibly brutal and sadistic witch, then you slowly realize that that was never the case at all and you start to genuinely feel sorry for her.

Envy from FMAB was my first choice, most of the original villains from Nabari No Ou also fit the bill.

Zabuza from Naruto probably counts as at least a partial example, SPOILER: Highlight text to read: realizing that he should have valued his protoge more than his vendetta. And tearfully saying his final farewells to Haku as he dies.

Anemone from Eureka 7's manga also counts, at least I think I remember her dying afterwards.

Genya from Giant Robo: The Day the Earth Stood Still...in the most tragic of senses.