Best stage 1 theme: A God That Loves People ~ Romantic Fall
Best stage 1 boss theme: Stirring an Autumn Moon ~ Mooned Insect
Best stage 2 theme: Song of the Night Sparrow ~ Night Bird
Best stage 2 boss theme: Diao ye zong (Withered Leaf)
Best stage 3 stage and boss themes: All of them. Really, I can't choose. ZUN always puts his best work in stage 3 for some reason.
Best stage 4 theme: Voile, the Magic Library
Best stage 4 boss theme: Love-colored Master Spark
Best stage 5 theme: Cinderella Cage ~ Kagome-Kagome
Best stage 5 boss theme: Lunar Clock ~ Luna Dial
Best stage 6 theme: Voyage 1969
Best stage 6 boss theme: Again, I can't choose. Since Touhou 6 was my first game, I'm partial to Remilia's theme. Lunatic Princess and History of the Moon are great too, though.
Best extra stage theme: The Centennial Festival for Magical Girls
Best extra stage boss theme: U.N. Owen was her?