Oh way too many, going to try and condense them.
In no particular order:
Geralt and Jacques' confrontation.
I remember the first time I saw Jacques, I was very skeptical and questioned the wisdom behind introducing a main antagonist in the last 5 minutes of the game. But as he kept talking, I kept on realizing that what he was saying was very familiar. From stuff like (paraphrasing) "didn't you say those with gifts should aspire to do good?" and "the elves are dying anyways, I'm letting them die on their feet."
Then it clicked and I realized who he was (before we see the medallion), and I remember having to pause the game and look awed at the screen for a minute. "I made him" was the general thought I had, and it took me a few minutes after finishing the game to realize the depth of the genius in this.
It's definitely one of my favorite moments.
Odrin.
I fucking love that guy and I don't know why. He's even become an inside joke between me and my brother, that is invoked whenever we drink beer. heck even in public, I'm always tempted to yell "BEEEEEEEER" when my pint arrives, and it's all because of Odrin.
I even deliberately delay my search for Odrin, just so that I can keep hearing "Ooooooooodrin, here boi, oooooodrin; OOODRINNNNNNNN" in an otherwise grim and muddy camp. I know it annoyed some people, but for some absurd reason, the screaming was like music to my ears.
BATS
Roche's commando wtf bamf moment.
Now of course first time playing, I knew that Roche was a crazy bamf, but that moment solidified it and I remember laughing.
I laughed because I was not sure what was the funniest. The casual "fuck" Roche utters before immediately launching himself on the nearest Kaedweni making it al looked planned, or the reaction that poor Kaedweni sod must have had to be attacked by a commando dropping from the sky, or Geralt's lack of surprise as if saying "yep that's my Roche."
It is a rare skill to be able to introduce epic and funny moments when the general ambiance of that part of the game was pretty grim, without compromising said grimness.
Now Philippa is awesomness made manifest, but one particular scene made her for me and that was the council.
2nd time playing around (first time was Roche's path), I admit I sort of forgot about Philippa and then I thought maybe it wasn't the wisest decision to confine her to one path as it may not be enough for her to rival or eclipse Sile de Tansarville. Boy was I wrong.
Now we all know dwarves are badasses. Does anyone even remember people talking shit about dwarves to their faces? But then we have Philippa simply saying "Please leave the thinking to me, Mister Zigrin. And I'd gladly hear less from you from now on."
It may sound trivial and maybe it is, but to me, this was the best way to introduce someone like her. Instantly I knew this is not a woman to be trifled with, that she oozed authority and power, that she doesn't need to yell or act intimidating to get her point across, that being intimidating is her natural state. That even dwarves know that they need to stfu when she is around.
The talks of Loc Muinne.
Of course from a story and plot perspective, the talks of Loc Muinne were a great way to unravel this huge web of political intrigue that's been woven throughout the game. But what drew me to it is the attention to detail and its subtleties.
From Shlard's small smirk when Henselt mentions the possibility of a future Nilfgaardian invasion, Radovid leaning forward and looking at Henselt as he put the blame of Anais' capture squarely on Dethmold, Radovid rolling his eyes at Natalis. Or Radovid keeping his composure when Saskia tells him Philippa escaped. Or Radovid's guards in the talks being Knights of the Order, and when Cardiun presents the charter, he does so first to Radovid whose consent is the one that matters.
All these little things add to the tension that is to be expected in a political conference. It also served a lot to add character to Radovid, who we don't see often before that.
Drinking Vodka with Letho.
My favorite protagonist - antagonist moment hands down. It was just so perfect. And it wasn't melodramatic, or with hugging, or some soft music, it was just right. Geralt drinking the vodka before Letho is the biggest show of trust one can show towards another, esp a deceiver like Letho. And I adored the game for letting me do that.
At the time, I had played another game that I felt had insulted my intelligence, something I do not take kindly, so when I was confronted with this scene, I knew then that the Witcher 2 was my favorite game of all time. Because in addition to it resolving the plot in such a brilliant way, and in addition to the characterization of Letho and his dynamic with Geralt, I felt respected. I felt my intelligence and my attachment to the story were respected.
Because when others would have allowed gameplay to dictate story and would have forced a boss fight against the main antagonist of the game, because that's how all games should end right, CDPR was like "no, we'll let you choose how to end the game." And when some would think that a non-violent ending is anti-climactic, what ended up being a conversation between two old friends and the sharing of vodka was one of the best endings I've ever experienced, and certainly the best antagonist-protagonist dynamic I've seen.
In fact I'd say that is probably my favorite Witcher moment, because it was then I knew the Witcher 2 was my favorite game.