I - Obtaining the airship to explore the "ancient" lands up north.
II - Leviathan! It's such a silly moment in an otherwise dark and homicidal-happy game.
III - Eureka! In the 3-D versions, the place is beautiful, has great music, and you get some super awesome weapons.
IV - Finally beating that dratted game! It gave me more troubles than fun. Maybe next time will be better...
V - Musical box. It's sad, but beautifully done.
VI - I haven't finished it, but so far the Ghost Train was a definite stand-out location for me.
...
X - Sin's attack on the ship and then the ocean village was such a heart-pounding moment.