The Unofficial Hierarchy of Touhou Music

Based solely on my opinion, listed from favourite to least favourite for each game. Also, title themes do not count (I only properly know two of them), neither do ending or credits themes (I've purposefully avoided listening to them to avoid spoilers).

Embodiment of the Scarlet Devil

 * 1) Septette for the Dead Princess
 * 2) Locked Girl
 * 3) Centennial Festival for Magical Girls
 * 4) Lunate Elf
 * 5) Young Descendant of Tepes
 * 6) Shanghai Alice of Meiji
 * 7) Pocket Watch of Blood
 * 8) Chinese Tea
 * 9) A Soul as Red as a Ground Cherry
 * 10) Beloved Tomboyish Girl
 * 11) Apparitions Stalk the Night
 * 12) U.N. Owen
 * 13) The Magic Library
 * 14) Lunar Clock

Perfect Cherry Blossom

 * 1) Phantom Ensemble
 * 2) Ink-Black Cherry Blossom
 * 3) Mystic Oriental Dream
 * 4) Capital City of Flowers in the Sky
 * 5) Fantastic Legend of Tohno
 * 6) Charming Domination (both versions)
 * 7) Paradise
 * 8) A Maiden's Illusory Funeral
 * 9) Ultimate Truth
 * 10) Necrofantasia
 * 11) Withered Leaf
 * 12) Border of Life
 * 13) Dollmaker of Bucuresti
 * 14) Crystallised Silver
 * 15) Doll Judgement
 * 16) Hiroari Shoots a Strange Bird

Imperishable Night

 * 1) Nostalgic Blood of the East
 * 2) Reach for the Moon
 * 3) Voyager 1969
 * 4) Plain Asia
 * 5) Illusory Night
 * 6) History of the Moon
 * 7) Lunatic Princess
 * 8) Extend Ash
 * 9) Retribution of the Eternal Night
 * 10) Eastern Youkai Beauty
 * 11) Lunatic Eyes
 * 12) Mooned Insect
 * 13) Dream Battle
 * 14) Love-Coloured Master Spark
 * 15) Voyager 1970
 * 16) Deaf to All but the Song
 * 17) Song of the Night Sparrow
 * 18) Cinderella Cage

Mountain of Faith

 * 1) Tomorrow Will be Sunny
 * 2) Japanese Wilderness the Girl Watched
 * 3) Faith is for the Transient People
 * 4) Gensokyo the Gods Loved
 * 5) Autumnal Waterfall
 * 6) Native Faith
 * 7) Dark Side of Fate
 * 8) Mysterious Youkai Mountain
 * 9) A God Who Loves People
 * 10) Candid Fiend
 * 11) Princess Inada is Scolding Me
 * 12) Road of the Apotropaic God
 * 13) Venerable Ancient Battlefield
 * 14) Cemetery of Onbashira

Ten Desires
Will be done as soon as I listen to the entire soundtrack so I can distinctively remember what each song sounds like.

Double Dealing Character

 * 1) Illusory Joururi
 * 2) Shining Needle Castle
 * 3) Mist Lake
 * 4) Exaggerated Castle Keep
 * 5) Primordial Beat
 * 6) Magical Storm
 * 7) Humans and Youkai Coming and Going
 * 8) Bamboo Forest of the Full Moon
 * 9) Reverse Ideology
 * 10) Kobito of the Shining Needle
 * 11) Mermaid from the Uncharted Land
 * 12) Dullahan Under the Willows and Lonesome Werewolf (a tie, since they're both too atrocious to listen to)

I don't remember Thunderclouds of Magical Power enough to rank it.