8-bit Theater gives us a Meta example (like the actual strip itself could ever pull one of these off.): The author faked an All Just a DreamGainax Ending for the sole purpose of pissing off the fans, expecting a ton of angry emails about the Anti-Climax. Instead he got a huge number of emails from readers expressing gratitude for all the work he had put into the comic, saying it was great while it lasted. He even got these from people who hated the ending.
Shortly after Black Mage becomes ruler of Hell, he just can't bring himself to tell Fighter that he didn't go to Heaven. In his words "Even though I'm the embodiment of all mortal evils, I just don't have the heart." He gets another one a strip or two later.
Fighter: I bet in Heaven they let you eat cookies for breakfast every day!
Black Mage: Yes. That is what they do.
This strip. Why? Because instead of murdering a person, Black Mage actually gave him a chance to back down. The clincher? It was Fighter.
The next strip qualifies, too, with Black Mage telling Fighter to just get White Mage away from him. Of course, it's immediately subverted, but still.
Although it may not be quite as touching as some of the other examples here, this strip (especially panels 4,5, and 7). Despite all the (often hilarious) horrible things they've done to people and to each other, there's something strangely touching about seeing three of the Light Warriors share a bed, with the sight rendering Drizz'l unable to kill them.
I think this strip counts a bit: I actually went "aaw" at the Light Warriors trying to cheer up Black Mage.
"You guys are almost as good to me as I deserve."
It does count... As a very twisted one, but still.
To extrapolate, Fighter finds a note written by Black Mage for White Mage explaining that he doesn't mean to act the way that he does around her, it's just that whatever he tries to say to her gets messed up and creepy on the way out of his brain and to his mouth. He recognizes this as a problem and doesn't blame WM at all for not wanting a thing to do with him. It is truly one of BMs few redeeming moments regarding their "relationship." Doubles as a Tear Jerker of sorts since it shows that BM has a shred of humanity under all the evil.
There's a subtle moment when Fighter faces off against the Fiends. At first it seems as though he's alone and being a Cloud Cuckoo Lander when he says the other Light Warriors are helping him. Then we learn that Thief and Red Mage are gearing up to fight the Fiends.
Thief and Red Mage briefly teaming up to protect White Mage against Black Mage. Made even more surprising and heartwarming by Thief's extremely uncharacteristic Heroic Sacrifice and then Red Mage's even more uncharacteristic last stand against Black Mage.
Remember, this is Red Mage and Thief we're talking about. When they see how far Black Mage has gone, neither of them even HESITATES to act like non-stupid non-evil honest to god HEROES