Yuri does an amazing job at chewing out Flynn when he helps Alexei capture Estelle
Yuri:Just what the hell are you doing? What happened to advancing as a Knight and fixing the empire from within? You've been nothing more than a damn puppet on Alexei's string. Don't you dare tell me that the Don and Belius died for nothing more than that! He was there working alongside you this whole time, Flynn! How could you possibly not know?!
Karol has one when proves himself quite a Determinator in the Blade Drifts of Zopheir, going up against a huge monster by himself to save the rest of the party, culminating in the part where he's flipped into the air by the monster, grabs a conveniently-placed BFS, and stabs the monster hard enough so that the party can recover and join the battle in full.
At one point, the game actually rewards you with an achievement for pulling off a CMOA-worthy finish with a Mystic Arte: Duke's second form in the final battle. Considering the wording of the achievement, it seems possible you can do it with anybody, but Yuri does it by, after his normal final slash of his Mystic Arte, jumping up in the air, shouting "This is it!" and hitting Duke with a super-sized Azure Edge.
Yuri's small speech to Flynn about his motivation for murdering Ragou and Cumore:
Yuri: The laws have always been the tools of whoever happens to hold all the chips.
Flynn: Just saying that doesn't make it right for individuals to judge right from wrong, or for you to operate out of your own private court of law! If the laws are at fault, then fixing those laws comes first. It's for that very reason that I'm still with the Imperial Knights!
Yuri: But you can't deny that lives were saved because those bastards were put down. You'd rather tell those people, 'Sorry you have to die today. I promise we'll change things real soon'?
Flynn: That's not what I'm saying at all!
Yuri: They're out there, you know. People so bad they'll just go on hurting others. What can the average person do but be victimized by people like that? You know it was the same way with our people in the lower quarter.
Not so much hypocritical as reformed, wouldn't you say? His Shut Up, Hannibal! doesn't come from a place of hypocrisy - it comes from understanding exactly what Phaeroh is doing, because he did it himself and grew up past it. It's simply Character Development. The fact that no one points this out is the only annoying part.
Character development or not, there's a massive difference between killing off individuals who are intentionally harming people and a person whose very existence causes her to unintentionally harm others, especially when her attempts to help the people around her in one way actually harms them in others. In other words, there's a difference between choosing and being, which is what differentiates Yuri's response from Phaeroh's. That key factor may be exactly why nobody pointed it out.
Yuri, Karol, Judith, and Rita, in succession, punching out Raven after he returns to the party after fighting them as Schwann. This may also qualify for Crowning Moment of Funny, especially Rita's line: "I didn't want to feel left out." Later on you find out that Estelle smacked him in the head after they explained things to her.
Along the same lines, the rest of the party (but especially Repede, Karol, and Rita) get one when the latter two punch out Yuri for trying to go solo for a bit.
Speaking of the post-Schwann boss fight, the entire scene is CMoA: with Raven revealing himself to be an immortal Death Seeker, then performing a (pseudo) Heroic Sacrifice to get his friends out alive. It manages to be so awesome, in fact, the the resulting Easily Forgiven scene works, purely due to the Rule of Cool.
Yuri and Flynn get a collective one when they beat the shit out of each other to resolve things - not because they're actually trying to kill each other, but because they're Heterosexual Life-Partners — uh, friends, and that's how they work things out.
Another Yuri/Flynn example: When they both plow through somewhere around 50 monsters to some of the game's best music to plant what amounts to a magic-nuke in the middle of a massive hoard, while having a casual conversation. The only down side is the fact that this is the only time you can have Flynn in your party.
Well, that and the fact that Flynn is horrible to control.
He's much faster in the PS3 version. He'd have to be, he's a permanent party member now.
Fighting Dhaos, Shizel, Barbatos, and Kratos from, respectively, Phantasia, Eternia, Destiny, and Symphonia is pretty god damn awesome in its own right, especially with their Mystic Artes: "Dhaos Laser!" or "Struggle against these holy chains! Shining Bind!"
This gets even more epic in the PS3 version: You now fight all 4 of them at the same time. As if that weren't enough, once you beat them, the rest of your playable characters all show up at once to fight you. They have boss-like stats and access to their mystic artes. How's that for an arena match?
Who can forget the last fight with Zagi? Upon defeating him he asks whether he should turn the rest of his body into a blastia as well. Yuri coldly replies with "Do it in Hell." before slicing Zagi across the chest and pushing him off the cliff. And all without even a change in expression. I mean, damn.
Fighting Kratos on Unknown. He is unquestionably the hardest fight in the entire game. Even the Fell Arms boss is nothing compared to how incredibly powerful he is. Kratos is incredibly fast, breaks out of combos with ease, hits incredibly hard, and when he goes into Overlimit, you have to run from him or he will slaughter you in the blink of an eye and then he'll will use Shining Bind; it hits for 30k damage. It's one of the most challenging fights in the Tales Series, but it feels to great when you finally win.
Dhaos was killed in his own game by Indignation. Programmers thought it would be received well by the Fans if Rita's Indignation was an instant kill when used on him. Certainly a CMOA for the programmers themselves.
And it manages to one-up the Sekundes thing. Did you think that Indignation dealing one-hundred-thousand damage was cool? Were you impressed by a player using Yuri to deal 2.5 million damage in a few minutes? Then you'd better be impressed with Rita dealing one point short of ten-million damage in one hit!
Oh, and to gain the Indignation attack, she has to basically reenact the opening to Tales of Phantasia. By going into overlimit 4 and using Thunder Blade on Dhaos, who appears in 200-man-melee, while he's at half health or less. She'll then spontaneously use Indignation (for the first time in that save file), and obliterate Dhaos in one final hit.
From The First Strike, Yuri overhears some Guild member boasting about how he ditched his client because the client annoyed him. Yuri (And later Flynn after one of the guild members drags him into the fight) kick the ass of almost everyone in the bar with just their fists. Also a Crowning Moment of Funny.