Stories with nonvillains

[Seiryuu]

OK, I'm looking for stories with a particular type of "villain", or "hero", who sometimes may be ambiguous, often appears to be a major bad, but turns out to have a real and really good purpose. Oftentimes he's a mole in the enemy's group, close to the top and seemingly a devoted follower of the enemy, but really just holding back his disgust and rage so he can subvert him and ultimately destroy him. Please put any examples in spoilers. The titles can be open or hidden, but please hide the names of the characters so people won't have a big issue literally spoiled.
A good example of this is

Spoiler:

the Harry Potter character

Spoiler for only if you've read or watched:

Severus Snape. Throughout the series, he's extremely suspicious, clearly hates Harry on some level and is bitter about him, and is very fond of black magic. He's shown to be a spy for the good guys, but his behavior is still so ambiguous that it's easy to believe he's just feeding them false information to hide the fact that he's actually a spy for Riddle. Any hope of redemption seems to vanish when he kills Dumbledore.
However, ultimately you find that he'd deeply loved Harry's mother and was doing everything to protect her son and destroy her killer, and he'd only agreed to kill Dumbledore to spare Draco the trauma of committing murder and spare his dear, terminal friend a slow and painful death. Harry even names his second son after him, saying that Severus was the bravest man he'd ever known.

Another (animie) example is

Spoiler:

Bleach character

Spoiler:

Ichimaru Gin. From his first appearance he looks downright nasty, and rarely lets up on his seeming evil demeanor. He betrays Soul Society and joins forces with Aizen, and seems to be completely loyal. The truth though is that he loves Rangiku Matsumoto and is determined to protect her from harm, and to personally destroy the one who had once hurt her. Thus, he protects Aizen to protect his love and to find Aizen's weakness, so he can kill him himself.

Nonvillains generally have unpleasant fates, but seem to embrace all the hell and bad karma they've accumulated for the sake of their true cause. The examples I gave are moles, but this might not always be the case. Any case where a character is ambiguous or apparently evil, and spends much of his part in the story as a "villain", in a brave or desperate attempt to help defeat the true enemy is fine.

[kitten320]

Do I have to name the character or just let you find yourself?
If no then here are the titles:
Katekyo Hitman Reborn fits perfectly with what you want, at least as far as I got into the series.
I think Inuyasha series kind of work too, sadly a lot of people still keep hating that character
Soul Eater has one character who happens to be good, but it was evil not because of revenge or something.

[Kotohono]

Two I can think of that might fit...

Spoiler:

Nanoha A's

Spoiler for Nanoha A's:

The Wolkenritter Knights are harsh and evil seeming until their objective/motivation is revealed, though they are somewhat re-deemed in the end, but not at no cost. Or perhaps even more so fitting it then the knights...

Spoiler for Major Major Spoiler:

Gil Graham who has the Liese twins act in an somewhat evil and deceiving way in order to force the dark form of the darkness out in attempt to have a chance to destroy it once and for all.

Katanagatari

Spoiler for Katanagatari:

I think Princess Hitei is almost this completely given her role in the story ultimately.

[Seiryuu]

Originally Posted by Konakaga

Two I can think of that might fit...

Spoiler:

Nanoha A's

Spoiler for Nanoha A's:

The Wolkenritter Knights are harsh and evil seeming until their objective/motivation is revealed, though they are somewhat re-deemed in the end, but not at no cost. Or perhaps even more so fitting it then the knights...

Spoiler for Major Major Spoiler:

Gil Graham who has the Liese twins act in an somewhat evil and deceiving way in order to force the dark form of the darkness out in attempt to have a chance to destroy it once and for all.

Katanagatari

Spoiler for Katanagatari:

I think Princess Hitei is almost this completely given her role in the story ultimately.

I haven't seen far enough on the second I guess. I completely forgot about the first; yes, that does fit a little, though

Spoiler:

they're misguided and seeking something they shouldn't seek, making them enemies throughout. The characters I mentioned before were after goals that the heroes could accept and support, given full knowledge. They acted villains and played the villain, and sometimes committed villainous acts, but the goal was to stop what they and the heroes knew was the true enemy. They knew what they were doing and wouldn't stop at anything, while the characters in A's would have likely pulled away if they remembered everything. On the other hand, the one in the major major spoiler fits another request I made some time ago, for an evil that must be awakened one way or another for any good outcome to be possible.

[mrShady]

Code Geass, but that might just be to obvious.