Events like the tsunami in Japan always bring out the religious and they say they are "praying" for those in Japan.
I don't believe prayer changes the events of the world.
I just know it makes people feel good and makes them feel like they are contributing something positive to the world.
I don't really know what to say when a person has experienced a death in the family except to say I'm sorry for their loss.
I'm not going to say some bs like, "Your loved one is in a better place" and all the other things theists say to someone who has lost a family member.
It feels weird to say, "You're in my thoughts" because honestly, what is that helping?
What have been your experiences in dealing with deal coming from an atheist's perspective?
What things have you said to believers that were genuine and helped them feel a bit better?
Sometimes I give a tiny crap what people think of me and I don't want them to think I don't care about their misfortune(s).
I had a few people in high school see me as "negative" because I gave my true opinion as to what happens to humans when they die. We just cease to live and eventually our bod rots away. No heaven, ho hell...we're just dead and rotting. Some of us are cremated.
Even though being in my thoughts won't help any, I still tell people that they are when something bad happens. It's not so much that they are hoping my thoughts will help, but the fact that it shows a sign that you care. Of course I'll offer my condolences and sympathies as well. It's also good to offer them someone to talk too as well. In some cases, what they may need most is simply a friend to talk with. When it comes to death, I always like to say that the person led a life well lived (where applicable) and to take heart in the fact that said person is no longer dealing with the suffering that likely surrounded the conclusion of their life. They may take 'not suffering anymore' in a way other than the literal sense I was using it in, but it still helps them feel better without me spewing some mutterings to a nonexistent deity.
For people who are completely unable to function due to grief, just taking over some of their basic chores is the most practical means of offering support, such as Misty has described. I typically put a big pot of soup or stew in their refrigerator, do their dishes, and return in a few days to freeze left over portions for them.
For those who are far away, the best I can typically do is an e-mail of condolences, with the typical lines already mentioned. Usually, when the person is sufficiently stable and up to coherent conversation again, I turn into a bit of an atheist vulture if they are the religious type. When they express sadness at their 'loss', I often ask them why they are sad if they believe is that they will see that person again in heaven. I rarely take it much further than that, but it is usually enough to make them question just how sure they are about their religious beliefs.
Praying hands are idle hands.
Religious people like the self delution of helping by praying instead of coming to terms with the fact that there is unfortunately nothing most can do directly.