Running rough
 

I have a 2004 Trail Blazer. I ran out of gas the other day. After putting gas in in it my truck is now running rough while it's I'd idling and the service engine light is flashings. What could it be?

Sometimes, if you let the tank get empty (or, if you usually drive with, say, less than a quarter of a tank), you have the risk of the fuel pump "overheating," because the fuel in the tank keeps the fuel pump cool...
That COULD be what happened to you,
but, of course it could be anything...
That's just a thought.
Could be a sensor issue, too.

what engine?

the engine is misfiring. start with having the codes read and post them here. the codes will help identify what/where to test first.