His penis hurts when he pees--what could be the problem?

Many possiblities: He could be passing a stone, especially if he's been having pain in his side or back. He could have an std like gonorrhea. He could have mild irritation around the opening where the urine comes out. The answer is is going to vary with the age of the person you're asking about, the circumstances and the associated symptoms. For anything but minor irritation, see a doctor for this.