Hard to choose and you already mentioned almost all mine:
- The cutscene before What Pride Has Brought. I loved all three counselors there. That scene is the answer of a wonderful team to a desperate situation.
- "Niceness before knives" after The Left Hand of the Divine, I loved what it meant and the delivery of the phrase.
- But my favourite one was In Hushed Whispers. Badass Leliana, truly badass, and with some of the most epic lines in the game: "I want the world back" "You have as much time as I have arrows.", "Though darkness closes, I am shielded by flame. Andraste, guide me. Maker, take me to your side!" and the aftermath with that bargain line.
I also love the light moments, that bunny shaped Lake Calenhad, that "Hush, just look pretty" to poor Cullen, "Those ruffles were very festive",... But In Hushed Whispers got me. Ok, Bioware, you already did a badass heroic ending scene for Leliana, now time to do the riding into the sunset one you stole from her.