Season 3's "Saving Face". Every scene with Bridezilla is screamingly funny, as is Taylor's initial reaction.
"Tapped Out," the whole episode. From the screaming witness to 'Detective' Richard Tracy to the speed-dating to Chief Pope's attempts to be 'one of the guys', it's comedy gold from start to finish.
"Chief, didn't you just get married?"
And the hilarious Funny Background Event of Tao and Sanchez betting on whether she'd call before saying "I do" or not.
Also, when Flynn is in the hospital in Season 6, instead of a "Get Well" balloon, his reads "It's A Girl!".
From that same storyline, Pope and Brenda.
Brenda: WHY WAS I NOT INFORMED —
Pope: *raises hand* How's Lieutenant Flynn?
Pope: Good. Proceed with your outrage.
Any time Flynn and Provenza share an episode, especially the whole saga of their part-time process server gig.
When Brenda finds out that the old widow who was going to sell her house to her and Fritz actually doesn't want to sell her house and pretends to do it only to have some people around to talk with. The top moment is when the lady buys Brenda's silence with cookies.
In the episode, "Fate Line" Claire, an intuitionist (psychic) and Brenda's future sister-in-law, tried to help Brenda find a killer with the help of a sketch artist. The resulting drawing ended up looking like Assistant Chief Pope.
The beginning of "Junk in the Trunk" that had the car that the body is stuck in the trunk getting loose from the tow truck, going down hill from the street, hitting an electrical post, and having a transformer fall on top of the trunk starting a fire.
Sanchez' reaction after he discovered that the woman that he had been flirting with and kissing is in fact a man.
Sanchez: Tell the chief that I'm going to therapy.
Brenda's reaction to Joel did not go quite as Fritz planned. She actually backs away from Joel and Fritz, terror warring with Cuteness Proximity... then her expression changes when she learns Fritz named him Joel.
"Living Proof, Part 1." Captain Raydor's wrathful return from the airport, dragging her luggage with her, because she has to investigate a rights violation and use of force complaint on an LAPD officer. Said officer? Pope.
Raydor: I have to make a report about a complaint on you, to you!"
All this while Pope and Taylor are chilling out and watching the game in the conference room.
And earlier, there's Raydor's reaction to Brenda introducing her as "My friend Sharon" to her parents.
And then there's all the times Brenda and Raydor interacting, first trying to pass off the case to each other, then their negotiations to enlist each others' help, and Brenda's reaction when Raydor arrives to talk to her suspect (who's a minor, and witness to Pope's complaint above): "It's a Christmas miracle!"