Pembleton and the unmarked squad cars. In the pilot, he forgets to write down the number of the one he checks out, and gets down to the garage only to be reminded that they all look exactly alike. His pride won't let him go back upstairs, so he starts checking the door locks of each.
Later, he's trying to get out of a parallel park job, but the cars in front and behind are too close. Bayliss is preoccupied with Crosetti's funeral arrangements while Pembleton, backing up, pulling forward, backing up, pulling forward, starts yelling "You can get it in, but you can't get it out!" and "I'm gonna shoot this car!"
The music montage in the movie with a frantic Mike Giardello uselessly running around and beating up suspects while Kellerman chooses to ignore him completely and to have lunch.
Pretty much anything John Munch says though his "Montel Williams" rant is definitely up there.
The detectives reading you your rights in "The Documentary".
Howard quitting Smoking and Felton's overreaction to it, and Bayliss getting Pembleton to smoke.
Munch ruining Bolander's and Howard's double date.
Lewis: You're like a father figure to me, big man.
Bolander: You ever repeat that, I'll gut you.
The "Electrolite Neutron Magnetic Scan Test" definitely counts.
Howard twitting Pembleton about her reasons for stopping smoking in "Smoke Gets In Your Eyes". Ed Danvers the "Alpha male", indeed.
Love at First Sight is represented with weird electronic stings and sudden camera zooms in "A Model Citizen". You might think the humour was unintentional, but then Tim and Emma meet eyes and crash into the furniture.
A child shooting makes Munch miss his alcohol awareness seminar. He calls in his excuse from the hospital, and the next day joins the class with his apologies.
"Oh, that's all right, Detective! It's not every day that an elephant squashes your mother!"
The time that Bayliss and Pembleton accidentally bust a major drug dealer with a truly massive amount of cocaine in the back of his car because they got the wrong pager number and believe him to be a small-time murderer.
Pembleton: You're not Manuel Rendares, are you? Bernard Weeks: Bernard Weeks. How the hell did y'all get onto me? I was so damn careful. I've been moving this kind of weight for 5 years and not so much as a traffic stop. Y'all DEA, right? Bayliss: No. Bernard Weeks: FBI, Customs? Pembleton: Nope. Bernard Weeks: Local narcotics. How long you been onto me? 6 months? Longer? You had to be on me for about a year, year and a half, to roll up on me with this kinda weight. Pembleton: Nah. We weren't looking for you. Bernard Weeks: ... Say what? Pembleton: We're not local narcotics. Bayliss: We're Baltimore Homicide. We're lookin' for someone else. This is just a ...a mistake. Bernard Weeks: A mistake? Pembleton: Yeah. Bernard Weeks: You roll up on me with 200 kilograms and it's a mistake?! Pembleton: Well, you haven't by any chance killed anybody in Baltimore lately, have you? Weeks: No way. Pembleton:[exasperated] We just wasted another day. Bernard Weeks:[stunned] A mistake? Bayliss: Yeah. Sorry. Get him outta here.