To me, Phantom Hourglass's soundtrack was a colossal disappointment. At least, as far as the bulk of the gameplay music is concerned - the dungeon and overworld themes heard throughout the entire game were the same repetitious three-note motifs for nearly every stinking location. Woo, this didn't get tired and repetitive at all!~
Cutscene music, on the other hand, was awesome. Captain Linebeck's theme comes to mind here. And then there is the boss theme, which may very well be my favorite in the entire series. Funny how these things work out, no?