Episode II, whose soundtrack is fairly mediocre overall, still has some of the best songs in the series, particularly those composed by Yuki Kajiura. Communication Breakdown, Fatal Fight, "Here She Comes", "Battle Of The Elsa", "Chase", "Sakura", "Sweet Song" ... real diamonds in the rough, no question.
Xenosaga Episode III's soundtrack by Yuki Kajiura is nothing short of amazing:
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.