One of the factors leading to Jon's suicide was the fact that his best friend since college had been a victim of the hijacking of Flight 11.
Season 2
"The Kiss": Gary punches the car of a guy who almost runs him over. When the guy stops and gets out of the car, Gary taunts him until the man pulls a gun at him. Fortunately, he doesn't shoot him.
A racial one for Rome in "We're the Howards". He is at a softball game where he is perfectly aware that he is the ONLY black man. While he is recording Sophie playing for his adoption video, a paranoid father thinks Rome is an ephebophile recording his daughters. He accosts Rome. Gary shows up, punches the guy, and it soon leads to Rome in the back of a police car with Gary.
Season 3
"Trust Me": Peter Benoit, a music professor who grooms his female prodigies.