47's rescue of Victoria at the end of Absolution and the hug they share after 47 kills Dexter.
Anytime that 47 shows any form of empathy, especially in Absolution where he vows to almost Papa Wolf degrees to take care of Victoria, promising that nobody would harm her ever again.
During the levels in the weapons lab, his Hitman with a Heart quality really shines through when he shows disgust at the idea of human experimentation and child soldiers. He even calls one of the scientists a monster and says his victims won't mourn for him.
47 going to the trouble of saving Father Vittorio in Silent Assassin. While he leaves his life of peace behind, it shows that he is not without a conscience.
Issue 34, full stop. What makes it great is that Garth Ennis, the writer, is notorious for hating superheroes, but he gives Superman one of the most sympathetic, sweet portrayals ever. Also worth mentioning is the two issue crossover with the Justice League of America, where Superman is describing a redacted story from the JLA's files to a reporter about Tommy Monaghan. Despite his dubious profession, Tommy was described by Clark as totally heroic and a good man at heart.
In the For Tomorrow, Ringo is facing nigh-certain death. Hacken tries to come with him, reasoning that they're partners, just like Tommy and Natt. Ringo, touched but also fighting to hold back laughter, can't bring himself to correct him, and manages to reassure him without endangering him, saving his life. Then Ringo gets into his car to go face his likely death with a fond grin commenting, about Hacken, "...you big, lovable hired killer you."