hard to say, so I'll list the reasons why I liked about each chapter
Chapter 1: well, I guess I liked the happy bouncy music of Petalburg meadows, and the battle music when you have to face Hooktail...
Chapter 2: definately the way the great boggly woods looked, incredible really... and the battle music for the Magnus Von Grapple (I absolutely adore Crump's theme)
Chapter 3: Glitzville's an excellent change of pace from the usual "do something in the village, go through a dungeon and face the boss" thing that's usually done in RPGs... and the Yoshi kid is neat as well.
Chapter 4: best... villain... EVER! Vivian's cool as well... and Twilight Town is awesome.
Chapter 5: another excellent chapter, Flavio, Cortez... they're all great, and Crump's theme returns!
Chapter 6: another great change of pace... in that the segment is about the journey to the village rather then doing something at the village.
Chapter 7: we're on the freakin moon! nothing bad about that!
Chapter 8: unbeleiveably creepy... I love it! the tower music is the best part... it's so cryptic and mysterious.