Always say "Bless you!" Or even, "God bless you!" when a stranger sneezes, that's just polite! Any other time, and it comes across as odd. Depending on context, I guess. And I'm sure atheists get a lot of "God bless you!" from people trying to be funny, so I'm not sure that's helpful! Would be better to buy them a cup of coffee and have them explain their beliefs to you. And hopefully you'll get a chance to respond nicely, in kind.