Jojo's Bizzare Adventure, the second arc of the manga. Nazis were researching an ancient race of vampiric supermen, ended up reviving one, and had to rely on the protagonist's group to defeat him. One of the Nazis gained the respect of the protagonist, and became a recurring ally character, never turning out to be an evil enemy insurgent. Nor do the Nazis continue trying to use the supermen for their own means - they appreciate the threat, and immediately begin trying to figure out how to destroy them. At several points in the story, the Nazis actually end up rescuing the protagonist, and are instrumental in defeating the antagonist.
While relations between the rest of the cast and the Nazies are suitably tense throughout, and there's a strong current of distrust and reluctance to be helped by them, the Nazi character was never shown to be a conventional moralist, or a man "forced to do unspeakable things against his better judgement, out of love for his country", as is usually the case. He is a Nazi because he believes in his leader - and yet, he's as well-rounded and likeable a character as any other in the series. It's the only instance of a Nazi character I can think of who's portrayed as neither an inhuman monster, or a saint who works behind enemy lines for the greater good.
Quite uncommon indeed - a portrayal of Nazis who aren't insane with lust for power, or meaninglessly evil. I thought it was interesting.