Episode II was a weird one. It had two composers: Shinji Hosoe, who took care of the in-game music and low-quality cinematics, and Yuki Kajiura, who took care of the music for the high-quality cinematics. The thing is, Hosoe's music was... shockingly mediocre at best, and downright unbearable to listen to at worst! Which is baffling considering Hosoe has shown in other franchises, both before and after his work on Xenosaga, that he's a competent composer. But on the other hand, the music by Kajiura is considered some of the best ever composed of all The Sixth Generation of Console Video Games.
Yuki Kajiura took care of Xenosaga Episode III all on her own, treating us with another amazing soundtrack:
Abel's Ark is also quite beautiful, and slightly unsettling. Also a Call-Back tune to "One Who Bares Fangs At God" from Xenogears.
The "Sakura" theme in Episode II and "Hepatica" theme in Episode III (arguably the themes for their respective games) are truly awesome. Not in the way to inspire awe and terror, but the way they draw out Tender Tears in how beautiful they are. The song "Testament" from Episode III can produce similar feelings... Well, at least the beginning part of it.