I don't know that there's any songs I don't like... I'll just go through this on a game-by-game basis.
EoSD: So many awesome songs. <3 Even if the quality isn't as good as the later games, it still has so many great pieces. One of my favorites musically.
Stages: 3,4,5,6,EX
Bosses: 2,3,4,5,6,EX
PCB: Not as much sticks out to me in PCB, but it still has some amazing tracks. I think I will agree that Yuyuko's boss fight and music choreography is epic win though.
Stages: 2,3,5,6
Bosses: 2,3,4,6,EX
IN: Amazingness. Great music here, there's a lot to love. Probably my 2nd favorite behind EoSD. Cinderella Cage, Lunatic Eyes, History of the Moon, Lunatic Princes... so much good.
Stages: 1,2,3,4,5
Bosses: 1,2,4,5,6a,6b
PoFV: Uhhh... yeah. I really just don't care much for the music in this game... it's all just remixes that don't do the originals justice. I will say that Komachi's theme and Fate of Sixty Years are great though.
MoF: I haven't spent enough time playing this game to really know much about the music, but Suwa Foughten Field and Native Faith are infinitely amazing, I absolutely love them.
SA: Besides having my favorite character in it (Parsee ftw), SA has some amazing music in it. Parsee's stage theme and boss theme are both golden. Sanae's stage and boss themes are greatness as well. I actually love Rin's themes as well.
Stages: 2,3,4,5
Bosses: 2,3,4,5
I would have to say EoSD takes the cake for me, with IN a close 2nd and PCB and SA tied for 3rd.