In first season episode “High Ground”, master sniper Gunnery Sergeant Ray Crockett, who’s gone vigilante (long story), catches the team who are supposed to catch him. He tells over their radio that they better bring body bags out here. The message is taken quite seriously as everyone assumes the Gunny to be Ax-Crazy at this point. However when the chopper returns it turns out that the gunny only took their gear and clothing, as they wear nothing more than body bags.
In "Pilot Error", Harm is attempting to clear the name of his friend, a deceased pilot, when he's blamed for a crash while testing a new auto-navigation system. He decides to fly the same mission, which involved making 5 "traps" (carrier landings) and then flying the auto-nav route. Harm's RIO is less than impressed with his landings.
(First hard landing)
Harm: Sorry, I'm a little rusty.
Lt. McKee: You're not rusty, Lieutenant, you're corroded.
(Fifth hard landing)
Lt. McKee: Thank God that's over, you're making me wish I'd joined the Air Force!
Related to the above, a number of episodes where a major problem could have been easily solved by calling the judge and asking him to reschedule a hearing were able to Hand Wave that away by pointing out that it was the same judge who was in the courtroom that day, and he still hasn't forgiven Harm for the incident with the gun.
There is a Running Gag where Harm is about to look at his watch, only for Mac to immediately tell him what time it is, down to the minute. Without having to look at her own watch. At one point, Harm just gives her a look, and she shrugs it off with "It's a Marine thing." US Marine Corps. Most Bad Ass timekeepers around.
The Screaming Birth in "Yeah, Baby." The entire episode is one Crowning Moment of Funny. Everything seems to go wrong. Harriet goes into labor on a high floor of the building while the elevator doesn't work. She tries to get down the stairs but can't. Harm and Mac get her into the Admiral's office. They get Mick to try to deliver the baby, but he reveals he only delivered sheep down in Australia. They get him out of the room. They get Tiner to try to deliver the baby, but he faints. Finally, enter the most unlikely midwife of all, Chegwidden. He promptly takes over and delivers the baby.