The Shadow Hearts series has incredible music. It might be best described as the result of putting the emotive and situationally-iconic music of traditional JRPG soundtracks into a blender along with the hellish noise horror of Silent Hill, turning it to "Liquify," and pushing the "On" button. Examples: one of many versions of Icaro, very much The Fate, Hardcore to the Brain (boss music!), Alice (you'll especially think so after playing Shadow Hearts: Covenant), and so much more.
Imbroglio. Not only is it one of the best final boss themes ever, but one of the greatest battle themes period.
The Three Karma. A strange song (even more so than Ladder to Heaven, which is already pretty strange), but nonetheless intimidating, dramatic, and glorious. The arrangetracks version also qualifies.
The first dungeon in Covenant, Apoina Tower, has a tune that gives a sense of mystery and intrigue as Nicolai and Karin delve into the story. Death is the Great Leveller is remarkably chilling and creepy.
As a counterpoint, the scene when Covenant's final dungeon becomes available is accompanied by the beautiful "~The Fate~ Cluster Amaryllis," a tune that starts out tranquil and then grows in power as Yuri calmly confronts the game's final boss. After Yuri is filled in on the Evil Plan, the boss then summons the dungeon and serenely tells Yuri that they will be waiting at the end.
Not to be outdone by its more famous descendants, Koudelka had some very atmospheric tracks.
"Requiem", which opens the game, is a lonely a cappella hymn which is a good parallel to Koudelka's own isolated existence.
A live version of "Incantation", in contrast to its grossly ill-fitting game version, truly sounds like the boss theme it's supposed to be. It really underscores how much vocals can add to a song.