I get really annoyed by this. Someone on Facebook, Twitter, whatever posts about issues they're having and the response from most people is "praying for you" or "sending prayers your way". What a cope out. I feel your actions are what define your intents. If you truly want to help someone get through a tough time, talk to them, help them, write them an email, whatever... Do something! "Sending up prayers" is the best way to feel good about doing nothing.
If you're sending up prayers, I assume you believe in God or some higher deity. Wouldn't they already know what's up? Shouldn't prayer be a personal thing between you and God? Shouldn't it be private? Yeah, Matthew 6:6 states it explicitly.