Warhammer 40k: Oh, I'm just joking, everything is morally grey there, so I could pick almost anyone.
In fact, let's do that (not all of them, but a choice few).
Tau are the easiest - sure, they are join-us-or-die(or-maybe-be-sterilised) space communists that might use mindcontrol on their allies and are controlled by a ruling cast of guys that can subtly change peoples opinions through pheromones, BUT they haven't had any corruption by chaos, actually ask you if you want to join and treat their people well, all the while fighting for the Greater Good.
The Inquisition might be shown as typical in-faction bad guys because they really like to call down an Exterminatus (a.k.a. FUCK THAT PLANET), but can you blame them? In a universe where a handful of Chaos-worshippers could doom AN ENTIRE WORLD and give it to the enemy?
The Eldar are ridiculed for some of their "EXACTLY AS I PLANNED" bullshit, seeing as they can do stupid stuff the plot requires only to see it paying off later. And also they would be ok with sacrificing all of humanity for a handful of Eldar. That too. Oh, and the also created one of the Chaos Gods just by being too hedonistic.
But... at least they see their problem. They actively try to live in a way that prevents them from falling to Chaos, by dividing their lives into "Paths", sections dedicated to a certain role. They don't kill unless it's necessary and they would be ok with humanity if humans weren't so genocidal and fanatic.
Chaos Marines... well, it depends on the Chapter, so I will just pick one. The Night Lords. They do horrible, awful things to people, and they have done so even back when the Emperor was still around. They claim they did it because everyone else was to afraid to do it and that it was necessary, and that the Emperor cast them out just for doing what he created them for.
And they are kind of right.
Don't get me wrong, they are still not good guys, but I can understand their feeling of betrayal. They helped unite humanity under the hand of their glorious Emperor, and they were cast out just for their cruel tactics.
I know another one, though: Some of the AAA-Megacorps of Shadowrun. Saeder-Krupp, for example. You know, the biggest corporation in the ENTIRE WORLD - all in the hand of a single mind: Lofwyr, a dragon. Now, in Shadowrun, dragons are known to think long-term. He is not a nice guy, and neither is Saeder-Krupp - they use the same tactics as any other AAA. But I have a book about the "Rhein-Ruhr-Megaplex", a part of germany, that is mostly in S-K's hand - and Lofwyrs claw. They bring work to a place with over 20% unemployment. The part of Essen they bought as Lofwyrs personal hort? It's safe to walk around there. In a part of Germany where that is really normally not the case.