At the top of my list would be Garak's basement scene in A Stitch In Time, in which he chooses to show himself out of the meeting he's supposed to be playing double-agent at, having lost his taste for the manipulative self-delusions and power plays of Cardassian society. It was a very powerful scene for me, Garak turning his back on the behaviours and belief sytems he was raised in but in a way that wasn't truly adverserial or aggressive. He wasn't concerned with any sort of posturing, nor was he being driven by pain or anger. He was simply withdrawing, politely and calmly, with a new understanding of himself and his current situation. Insight and revelation, and not overblown or wrapped up in passion, instead arrived at peacefully. The scene's resolution gives a sense of simple but deeply affecting "rightness", of positive change and lifted burdens, rather than triumph or apathy or heady freedom or any of the other emotional states you might be expecting from a "turning your back on your prior life" scene. It isn't even truly "satisfying"; it's deeper than that.
I love the scene because - How can I put this? You know Bilbo's line in The Lord of the Rings about how stepping out your door is risky business because who knows where you'll be swept off to? Well, while his point was nothing like mine, that's a useful line to have in mind. Without change, there's no life. But to someone who's wary of the currents and chaos of the path outside, any sort of development seems too dangerous. To have a character making positive change, identifying problems while moving himself away from them (and more importantly away from participating in them or reproducing them in himself) without having to throw himself into those currents...it's like finding a third dimension when you only knew two.
Another "greatest moment" would be the scene in Destiny: Mere Mortals that leads into Hernandez' attempted suicide. The sense of dislocation and emotional distance from the Caeliar around her came through very effectively. That entire book was masterful in its emotional power (Hernandez' story is one of Trek lit's most memorable), but this was one of the most striking scenes. If Garak's scene felt simply "right", Hernandez' perspective here just felt "wrong". As it was supposed to, of course.
Finally, from the Prophecy and Change story by Una McCormack, the last line, in which Kira joins in the cry of "For Cardassia!", "and meant it". It's one of the greatest and most emotionally satisfying character moments in fiction (to me anyway) and I'm surprised more fans don't mention it. Kira Nerys is high on my list of favourite characters, and if there's a moment that demonstrates both the content and the development of that character in a more straightforwardly effective manner, I haven't found it yet.
Hmmm, looking over that, you can tell I have a thing for profound, perspective-shifting character moments delivered in simple or understated ways - either those that show us the shift or which draw attention to shifts that have taken place, however quickly or slowly.
