For certain values, those values being
my view of good and evil (since that's certainly debatable topic) and
my belief in the nature of animal emotion and thought (also a debatable topic), I can give this question a definitive "Yes."
There are many stories like this one:
http://www.youtube.com/watch?v=ofpYRITtLSg&feature=player_embedded where an animal (in this case, a dog) does something unnatural for its species, showing, IMO, both reasoning and emotion, to consciously do good in the world.
And there are also stories (that I have no desire to seek out or link to) where they go just as far out of the norm to do evil.
I have had a horse fight a pack of dogs for my safety, and have seen a skittish horse stand stock-still when jumped on from above by my small son. I've seen a dog who loves to hunt lick and stand guard over a baby possum, and a dog who had long since given up puppy-rearing produce milk for an orphaned puppy. To me, all those actions showed either reason or emotion that I would consider "good".
On the other hand, I've seen a pack of dogs tear a cat limb-from-limb for nothing more than sport, leaving pieces of its mangled body everywhere and slinking away afterwards, tails between their legs (I was about eight at the time, and this pack wasn't mine.) To my mind, that sort of senseless destruction, not for food or even territory but simply for the thrill, is "evil". And it's not the norm in animal society any more than it is in human--if, indeed, we insist on separating the two.
I would say that I don't think an animal would have the thought process equivalent to "I will do this, because it is good" or "I refuse to do this, because it is evil", but on review, I can't even make that distinction. Generally, I would say that the rules are what matter, as in a dog working VERY hard not to pee on the floor of a locked house because it would be "bad"--"bad" here
mostly means "against the rules". It's a matter of trying to figure out how a dog figures "good and evil", and now we're WAY too esoteric, because you'd have to believe as I do to get that far.
But not too long ago, there was a study done (I'll try to find and link it later--right now, breakfast calls) where dogs who had been taught to sit on command, and did so reliably, were split into two groups. Both were commanded to sit, but only one got treats. The non-treated dogs soon started refusing to sit, eying the treats of the others, presumably because the treatment was unfair.
When the experiment was repeated with Apes, they got similar results, except that while for dogs, the only distinction that mattered was "treat/no treat", Apes would cease to preform if one group received a treat that was perceived to be "better".
To me, this shows a sense of fairness, and a willingness to operate against "the rules" if they are perceived as "unfair". Since I have also seen animals "act out" (such as a housetrained cat peeing ON THE STOVE BURNER or a dog who literally peed ON THE MAILMAN that he hated) in ways that were clearly against the rules, but also seemed to be protests against "bad" things, be it "unfairness" or just things they saw as "bad", I believe they have at least a sense of "good" and "bad" that goes beyond the rules, and that this judgement originates within them, from their own thoughts.