YAY self-indulgence!
By far, Frozen Mountain and FM2 (the old one, not the new one as much). Those levels - particularly FM2 - are absolutely incredible. I think FM2 is my favorite level ever.
However, I do also very much like Si's Rememberance and the other one... those levels are very long and pretty difficult, but they for my money capture the mood beautifully.
Nifflas's Strange Dream, definitely.
I'm not a great fan of Colors, as good as it is. I really like the green area, and beautiful music, but the rest of it... meh.
I used to love Sky Flower, but it's a bit short.
Probably some I'm forgetting.