The old "I'll pray for you" bullshit really upsets me when I'm going through something traumatic. Sorry, not sorry but that is not what I need to hear during my time of pain. Stop trying to shove your religion down everyone's throats. Its not helpful in any way to an atheist and its rather insulting that you know who you're talking to, that they are in pain and yet you selfishly take an opportunity to try and be all preachy. Don't. Just don't. Your silence is better than your prayers to your god.
Disclaimer: I am only responsible for what I say, not what you choose to understand.