"The Poisoned Chalice" / "The Assassin" has several:
Cesare starts off with a couple in the pilot—in particular "wringing the neck" of the metaphorical monkey that wants to bite his father (you'll get it when you see it) and proving that he will do anything to protect his family.
Vannozza's thundering rage when she finds out Rodrigo lied to her about having to be chaste and taking up with Giulia Farnese. The woman marches into the Vatican and slaps the Pope.
In "The Art of War", when Lucrezia takes all of the things she's learned from her family and Giulia about manipulation and her innate power over men and plays King Charles of France like a Stradivarius. On the day that the massive French army meets the much-smaller and badly-trained forces of Rome, Lucrezia watches the French cannons cut apart Roman soldiers and orders Charles to stop. She rides across the field of battle to speak to Juan, telling him to allow the French bloodless entry into Rome. She rides back and informs Charles that since his "real" target is Naples, he has no reason to harm Lucrezia's home when it will allow him entry, does he?
And then there's the moment when she makes Della Rovere hold her horse. All that he has done to get this far, and she dismisses it with a smile and a proferred bridle.
Rodrigo gets three in "Nessuno":
First is his master manipulation of Charles. He greets the French king not in his full Papal regalia, but in the robes of a simple priest. Charles even mistakes him as such when he walks into St. Peter's. He uses Charles's own piety and dreams of recognition to get him to agree to abandon his war against Rodrigo and crowns him King of Naples to boot.
Cesare beating his brother, the soldier, in a sword fight.
Della Rovere kills two highwaymen, both while lying prone in a cart and one of them at range. He even tops it off with a Bond One-Liner.
Forgive me, sister. Sometimes goodness needs the help of a little badness.
The reveal of Rome's "cannons" is awesome from start to finish. Cesare's defiance, the pounding music, the synchronized falling-away of the banners unveiling them, and not least the actors' work—hardened political mavens and soldiers having subtle but uncontrollable flinches in the face of the sudden appearance of massed artillery, men ready to fire them, and their battle lines still forming up and well within range.
The best part of that? The cannons are all fake! When it was clear that Rodrigo's financial mismanagement made it impossible to cast real ones, Cesare had them made out of plaster instead. The part where he reveals this to his family is also brilliant, as it drives home to Rodrigo a) Cesare is someone he truly can rely on, and b) just what a house of cards their dynasty is.
Lucrezia's cooking lesson in "Stray Dogs". A young girl, barely much more than a child, able to give a lecture on morality, financial management, and responsibility to the entire College of Cardinals.
After lightning causes the roof of a church to collapse near the end of “The Choice,” killing several people, the uninjured clergymen make their ways outside. Rodrigo, having just accidentally caused harm (and soon after, death) to befall a young boy while trying to order him to safety, pleads with them to return back inside the unstable building and help those who are still alive but trapped. One of the clergy speaks up, claiming what happened is the judgment of God. Rodrigo throws it back in his face, saying God will judge them for what they do now and goes back inside.
It's pretty gory, but seeing Giovanni Sforza get what he deserves in "The Choice" was pretty awesome.
Lucrezia effectively telling Rodrigo to piss off when he says he's planning to marry her off to someone else. Particularly the bit where Rodrigo tries to condemn her for her "ingratitude" and she very calmly lets him know what she thinks of that, and the last marriage he arranged for her.
Juan captures Caterina Sforza's son and tortures him while she watches from her city walls. Does she surrender? Even with her son's screams ringing in her ears and tears on her cheeks? Does she heck. "I will never, NEVER bend my knee to the whoremaster of Rome." Then she tells Juan that she can bear ten vengeful sons for every one he kills, and shows him just what she'd do it with. In other words, she lifts her skirt and flashes Juan and his army. And the best part is, it's based on an actual legend...that sadly has no real veracity, but it's still absolutely brilliant.
Juan's capture of her son itself is pretty awesome, especially for him. Yes, he's clumsy, and stupid, and cowardly, and it doesn't actually work out in his favor, but for just one moment in the entire series he actually lives up to the Borgia name by changing the game on his opponent through sheer cunning and ruthlessness. The camera even emphasizes Caterina's shock and his determination.
After Savonarola badgers Cesare and Machiavelli, mocking them and giving not-so-subtle threats, they leave the bonfire of the vanities. He turns around...and is face to face with Micheletto, whose expression is so like that which he wears when he kills someone, and who (as a gay man, if one who hides his nature) is threatened by Savonarola's policies, that the viewer might, for a moment, think that Savonarola is about to join Giovanni Sforza. And this firebrand, a man of absolute faith and confidence in God and his own unassailability in Florence, surrounded by his own flock...is, for a moment, terrified by nothing more than a look.
Later, once Savonarola is imprisoned, he attempts to taunt Micheletto with what he assumes is his greatest weakness — and gets a Bond One-Liner in response:
Savonarola: I know what you are. I have had your kind stoned to death, and their corpses dragged through the streets. ... Men who lay with men. Sodomites, who corrupt young, innocent boys — who artists use as angels. I have cleansed Florence of her sin.
Micheletto:[reaches slowly through the bars, causing Savaranola to shy away in fright] And yet here I am.
Cesare also deserves props for walking the streets of Florence without an armed escort and wearing his full cardinal's regalia so everyone knows who he is; he knows full well that the mob could turn on him at any moment, but walks among them anyway.
You gotta hand it to Savonarola. He may be a tyrannical zealot and iconoclast, but walking between two huge walls of fire takes equally huge balls. And even when he fails to walk through it untouched by the flames (duh) and, disgraced and disfigured, is taken back to Rome in a cage, he still has enough gall left to tell Cesare he’ll be an old man before he manages to torture a confession out of the friar.
The anathema of Friar Savonarola interspersed with Savonarola's trial by fire accompanied by Ominous Latin Chanting . In particular, Cesare's defiant face as he watches the friar try to make his way through the flames.
Is it wrong to consider Juan’s murder as one of these for Cesare? Hell, even Micheletto tells him he’s in awe.
Just generally, Hernando de Caballos. A Conquistador General brought back from Spain by Juan, he manages to drag something salvageable out of a disaster, and then calls pretty much the entire Italian Nobility out on their politicking. To Cesare's face. And lives. Notable for being both a badass and smart enough to get out while he still could.
Lucrezia defiantly telling off her father (and to some extent her mother) following Juan's death. She doesn't care about Rodrigo's hurt feelings and shock—because he did not stand by her after Paolo's death and she is finally asserting that and his hypocrisy. As Cesare comes to stand behind her, he delivers his own awesome moment, coolly explaining how he wept for Juan and can spare no more tears (with no small amount of irony). And finally, unmoved by their father's grief, they walk out together, cementing something that has been building since the beginning of the season: their break from their parents' arms and the forming of their own, much crueler and pragmatic, faction of the Borgia family.
King Charles of France besieging Lucca. When it's mentioned that the city wants to discuss terms, he simply has his artillery fire at the gates, blasting them down completely. He then points at it and says "Those are my terms." then has his army storm the city.
In Season 3's opening, The Sforzas plan to murder all the Borgias in their houses. Unfortunately for them, they did not account for Micheletto: The second he notices something slightly off place, he catches on the entire plan, escorts the family to safety, sets a trap and murders the assassins effortlessly.
Lucrezia also gets props for singlehandedly saving Rodrigo from a poison that everyone (including the physician,) thought would be fatal.
The moment in "Siblings" when Caterina Sforza and Rodrigo Borgia come face to face for the first time. Caterina, the Magnificent Bitch, has just plotted several attempts against Rodrigo and his family, tensions are at an all time high, and she parades in on her horse at the steps of St. Peter's. She kneels before Rodrigo and kisses his ring, but not before proving precisely why she's a worthy foe:
Rodrigo: We had almost given up hope of seeing you kneel before us.
Caterina: I bend the knee before no man, Your Holiness . . . except when I wish it so.
Caterina, despite the death of her only son, gets another one in 3x08. The audience is led to believe that it's the 'Turin Shroud' she sets up in Marino to draw funds from Rome, but tt's revealed that the newly crowned King of Naples is her ally, and he's been given instructions to hold Lucrezia and Giovanni hostage should Cesare march on Forli with the French army. And this comes just hours after Rodrigo Borgia gave Frederico his blessing to be King! In one fell swoop, she's secured her city, avenged the death of her son, and has captured the only two people that Cesare unequivocally loves.
Rodrigo sends Cesare to France to secure the king's alliance in his coming war with Sforza. He expects Cesare to return with enough gold to replenish the Papal Armies. Cesare returns with the French Army itself. Even better, the sight of such a formidable force is more than enough to make Caterina Sforza's allies turn around and join Cesare instead.
Overlapping with Crowning Momentof Heartwarming, we have Micheletto murdering the King of Naples for refusing to allow Lucrezia to bring her child with her to her new home.
Lucrezia convincing Prince Rafael, heir apparent to the throne of Naples, to give up his claim to the throne so that his much nicer, more easily manipulated half-brother can be King. She does this in several steps: first she saves the younger boy's life from a botched poisoning attempt, locates the woman who sold Prince Rafael the poison and threatens to make it public knowledge that Rafael attempted fratricide. And she makes it more than clear that she'll wrap her daddy - the freakin' Pope - around her finger and make it so that he will never give his blessing to Rafael to be King of Naples. Rafael weighs his options and decides to leave, though not without threats. Subverted when it turns out that she chose the wrong brother...
She gets one earlier in the episode, when she chastises Rafael for failing to murder his brother. When he's had enough of her accusations, Rafael actually puts his hand around Lucrezia's throat, warning her that she's on dangerous grounds. Lucrezia's response?
Lucrezia: I'm aware: you have your hand wrapped around my throat. *casually removes his hand* Failed again.
Cesare killing both Ludovico Sforza and Caterina's son Pedro. It goes against his father's wishes, but in one fell swoop, he secures Milan for the King of France and hurts Caterina politically, militarily and personally.
Federico showing that he played Lucrezia and the entire Borgia family like a harp may be a general Kick the Dog moment with the glee he took in it, (and a literal Kill The Dog when he convinced her to support him), but the fact that nobody else has ever gotten the better of Lucrezia in such a way gets him some points.
Lucrezia poisoning the entire Neapolitan court with a sleeping drug so that she can escape.
Rodrigo buying the entire Italian supply of sulphur, making it impossible to make gunpowder, and neutralising every force that could oppose him at a stroke.
The Siege of Forli. Micheletto comes back to say goodbye...and to point out the weak spot in Forli's walls to Cesare. Five or six cannon shots into the ground near Forli's gates, and the entire wall comes tumbling down. The battle is more or less decided at that point.
Or earlier, when Cesare's French Army takes Caterina Sforza completely by surprise, appearing on her doorstep before she has time to gather food or supplies for her people.
And just because Cesare wins, doesn't mean that Caterina goes down without a fight. She is determined not to be taken alive by Cesare, and is prepared to hang herself on her balcony, taunting Cesare to give her a legendary death and then laughingly wondering 'Does it take a Caterina Sforza to kill a Caterina Sforza?!'. And even when that fails, even when Cesare escorts her to Rome in a literally Gilded Cage, what does she say to the Pope when he finally has her cornered and without her 'claws'?
Caterina: *in a calm, collected voice* Don't be so rash, Your Holiness. I still have teeth. *nearly bites Rodrigo's hand off*
YMMV on that one. At that point she's been thoroughly humiliated tactically, the walls of her fortress are in ruins and her forces are completely bottled up and practically defenseless, and then she climbs up on a wall and threatens to hang herself, boasting hysterically that nobody could possibly kill her but herself just because she knows that they intend to take her alive, which they succeed in doing despite her antics a moment later. Her stubbornness in resisting and condescending even though Cesare foils her plans and outwits her again and again can makes her seem more childish, self-important and stupidly prideful than courageous. In the end, she was only a serious antagonist because she allied herself with existing enemies of the Borgias, refused to be bargained with, and launched a bunch of failed plots while they were busy with other things.