Season 1

When Valeria asks Escobar for her share, he just replies "No, my queen... The thing is, you are in this for love, aren't you?" and pats her on the ass.
When Murphy and Peña go to a Columbian brothel to arrest a former CIA pilot who now works for the Cartel, we learn that it also happens to be Peña's favorite brothel. Several of the prostitutes who work there greet him by his first name.
Peña: I-- A friend of mine told me about this place. I've never been here before.
Peña repeatedly fails to shoot down a homing pigeon. Murphy takes the shotgun and shoots it down easily, much to Peña's shame.
Murphy: Ever been duck huntin'?
Peña: No, I have not been duck hunting, you... fucking hillbilly.
- A bit earlier in the scene, when the two were watching for a pigeon to fly out, Murphy pours himself the last of his coffee from a Thermos. Peña takes the cup and takes one sip, shakes his head, and unceremoniously pours it on the ground. Must've been American coffee.
Some Black Comedy as Escobar follows a funeral over a satellite phone while the resigned priest goes about it with another phone mere feet away from his mouth.

Season 2

During a Walk and Talk, Peña passes by a saluting female soldier, as soon as he realizes it, he looks back with his characteristic leer.
An intentionally bad tip leads Murphy and Peña to George H Bush.
Maricas!
Escobar goes editorial, much to Murphy's delight.
Murphy: When Pablo Escobar starts believing the pen's mightier than the sword... you know you're getting to him.
Peña trolling Quica on the phone, in order to locate him. See this link.
There's something darkly hilarious about Escobar's attempts to intimidate Germany into granting asylum for his family, mostly because it comes out of nowhere. It sounds funnier in Spanish than English.
Escobar: (over the phone) I'm going to shove bombs up your assholes, you bastard motherfuckers. Nazi, racist gonorrheas, I'm going to kill you all. You hear me? I'm going to kill you all!
During most of the season, Murphy's much-maligned Lemony Narrator schtick from Season One is heavily toned down, with his voiceover largely reduced to historical exposition. Then in the season finale he starts slipping back to his old habits...and is abruptly cut off by the bullet that kills Escobar. He doesn't say a single other word in the episode's remaining few minutes.

Chepe guns down a rival Dominican gang in a beauty parlor, with a machine gun hidden under his smock. This ends up setting the smock on fire, and he has to fumble for quite a while to get it off.
Pallomari has to give some money to the agent responsible for his extraction, so said extraction doesn't constitute kidnapping. He quickly gives away all the cash he has in his wallet, but when he's told it's a technicality, he replies "well, if it's only a technicality..." and recovers most of it back, except for a few minor bills.
Pallomari clearly enjoys every second of testifying in court, letting his ego and smugness run completely on free-wheel.
Lawyer: And you were an accountant for the Cali cartel?
Pallomari: No, I was the chief accountant. The chief! El jefe!

Hernin Naranjo's hilarious 1970's dress and haircut◊. Doubly so when his brother seen later in the episode is sporting the exact same look. When Hernin shows up, some viewers were actually rooting for something terrible to happen to him between his terrible haircut and disrespecting Félix.
Rafa viewing the mansion and emphasising to the real estate agent he needs a place he won't be, um... disturbed by anyone. Cue loud engine noises... and Rafa and his goons racing through the halls on motorcycles.
- In a later episode, a motorcycle is seen in the background at the bottom of the pool.
Don Neto and Rafa having a cocaine party, with one the highlights being Neto going crazy while playing "Karma Chameleon" on a CD, excited that the CD player is not affected when they jump.
Escobar has a tense meeting with Félix where he declares his dislike for Mexicans and that he could feed Félix to his hippos. After a deal is done, Félix chuckles nervously and asks Escobar if he would have actually fed him to the hippos, and Escobar responds that he wouldn't have, because "hippos don't like Mexicans either."
Kiki concluding the unofficial interrogation with the cartel banker, pressuring him into working for him, with a big fake smarmy banker smile and voice.
Kiki: Why don't let your money work for you?

For his fortieth birthday, Félix is given a live tiger as a present. Besides Félix's general confusion about what he's going to do with a tiger, the marching band that brings it in starts playing a marching band version of "Eye of the Tiger", and El Chapo dances to it.