(Forgive the rant, but this is a big question. Also bear with my reasoning, I still only own one game).
Unlike other questions, I'm not going to judge purely on musical value, but on the song's value as a theme; now well does the song do its job. With that in mind, my winner is
The Gensokyo the Gods LovedThis song screams "paradise," which seems to be the unofficial nickname for Gensokyo, and the stage itself does this perfectly, starting off with a pure red-orange background before opening up to the base of the mountain: a beautiful river surrounded by the colors of the season. The main chorus halfway through (midboss) with the trumpet and piano is one of the most triumphant and beautiful in the series, and marks one of the only times outside of Nuclear Fusion that I like Zun trumpets. The post-chorus flourish perfectly illustrates the large fairy counter-attack and storm of bullets that accompany. Overall, this theme describes it's stage, and Touhou as a whole, perfectly.
Honorable MentionsLuna Dial- Lunar Clock: Musically among the weakest in EoSD, but as Sakuya's boss theme when played with the fight it fits. The normally stoic maid comes at the intruder with everything she has, and the music drives this point home sharply (get it? Sharp? Point? Kni- *shot*)
Green Eyed Jealousy: It's very, very rare that a boss theme accentuates the boss herself, but this song does it. And the remixes?
These two propelled her from near bottom-of-barrel into my top 5.
There are many other great themes, mostly anything I've already voted on. Nuclear Fusion, Primal Scene, Illusionary Night, UFO Romance. So many good songs in this series! :V
