Yes...any scene is good in CT. But some do rise above others for me.
One: Kingdom of Zeal
It's just beautiful, and majestic. Everything is so vividly different, and not only from the Earthbound village. It's different from any other place. Yes, I could go on and on about it, but there is much talk of Zeal elsewhere here. Go read it.
Two: Ocean Palace
After defeating Dalton and following him through the warp, ooooh. Gives me goosebumps. I have the Ocean Palace song as a ringtone. I just love when you first arrive. The music, the dark, marching forward towards Lavos, being underwater, it's all so...cool.
Three: Black Omen
The whole place is pretty sweet, but it's the last area, having bested everything else, walking into a hall and seeing yourselves floating there in front of you. Eeeeeerie.