I've never seen anything about pilots fighting during the flight but on Air India 611 they fought before the flight then proceeded to fly anyway. There are differing accounts of whether it was physical or just verbal. The captain claims he was punched for calling his older copilot "uncle."
On Express Jet 4453 apparently they got into such a heated argument that when they landed, the flight attendant made the passengers disembark. They continued on in a different plane with a different flight crew.
There are reports of a fight between pilots on a China United Airlines flight but finding out what actually happened will be difficult.
On JetBlue flight 191 the captain started ranting and raving to the point where flight attendants and passengers had to remove him and physically restrain him for the duration of the flight. There's video of the incident. He was charged with interfering with a flight crew but was found not guilty by reason of insanity.
And on Delta 2598 the pilots did an emergency landing when two flight attendants got into a brawl.