I understand that faith is very important to many of my religious friends. As annoying as I might find their blathering about prayer, it would not be appropriate to express this sentiment in the midst of their distress. But like Stardust says, I'm not always sure what to say instead.
Sometimes, I'll say something along the lines of how I'm thinking about them and hoping for the best. But that seems weak when others are promising to engage in superstitious rituals to bring about divine intervention on their behalf.
Maybe I should offer to send up some "burnt offerings" or animal blood. The Old Testament makes it sound like that is the solution for virtually all ailments. But of course, I don't believe any of that garbage and have little interest in pretending otherwise.
What do you typically say in such situations?