Found this discussion of Trigun on the atheism discussion board of Reddit today: "Where Do You Get Your Morals?"
I haven't watched the series, but it sounds intriguing, and perhaps good for an atheist audience. Here are some of the comments:
'I think the show is a good presentation of moral dilemmas. Rewatching the show several years later, I think I agree with Knives' idea of saving the butt…