One of the sucky things about being an atheist is you don't get to feel like you're helping people as often as theists do. For them, hearing about someone's tragedy or difficulty triggers an instant response: "I'll pray for you." Now, a lot of people will do something substantive in addition, but there is a certain danger of complacency in believing that mumbling to your invisible omnipotent friend can have an effect in the real world.
Luckily, just telling someone you're thinking of them, sympathizing, and pulling for them does offer some real solace. So in that respect, whether you say, "I'm praying for you," or "I'm thinking of you," or "Damn, that totally sucks," or "I'll sacrifice an unblemished calf for you," the person hearing it does get some help.
Lately though, I've been lucky enough to be able to help for real: babysitting a friend's daughter for day after the friend's mother died unexpectedly and she had to deal with the logistics of death as well as the emotional load; taking dinner to a friend from my moms' group who almost had to be hospitalized for depression last week, and having her over today so she's out of the house and not isolated.
As hard as it can be (that was one looooong playdate, let me tell you), it feels good to do something substantive to help. And I like to think that my humanism inspires me to do so in two ways: valuing other people, and realizing that there are no magic words that will change their situation.