I thought it would be interesting to get an idea of what people liked best for each theme, so TOPIC!
Anyway:
Menu Theme: Sealed Gods (MoF). Just...nice.
Stage 1 Theme: Dream Express (MS) takes this one for me, though Ghostly Eyes from IN comes close.
Stage 1 Boss: A Tiny, Tiny, Clever Commander(UFO), no question.
Stage 2 Theme: Song of the Night Sparrow(IN). SA's is also up there.
Stage 2 Boss: I'm going to go with Deaf to All But the Song(IN). Mystia cleans house.
Stage 3 Theme: The Gensokyo the Gods Loved(MoF). PCB's gets an honorable mention.
Stage 3 Boss: Doll Judgment(PCB) grabs this one.
Stage 4 Theme: MAPLE WISE(MS). Nothing else comes close; I'm not much a fan of the Stage 4s for some reason. Heartfelt Fancy is the only other one on my mp3 player.
Stage 4 Boss: Now they start getting tough. I think Phantom Ensemble(PCB) grabs this one, narrowly edging out Forbidden Magic(MS, though I don't care for Mai or Yuki's themes) and Maiden's Capriccio(IN).
Stage 5 Theme: Probably Lullaby of Demonic Hell(SA). Difficult, as I like every stage 5 theme except Kagome, Kagome.
Stage 5 Boss: BIAS! Lunar Clock ~ Luna Dial (EoSD) is hands down my favorite Touhou track, so it wins this one.
Stage 6 Theme: ...ouch. Hard to choose, but I think Voyage 1969(IN) narrowly edges out MoF's.
Stage 6 Boss: I have to go with Suwa Foughten Field(MoF).
Extra Theme: Centennial Festival for Magical Girls(EoSD). I love that track. Alice in Wonderland (MS) and Tomorrow Will Be Sunny(MoF) are close, though.
Extra Boss: Reach for the Moon, Immortal Smoke(IN). In my opinion, ZUN's finest piece of music in the series. Hartmann's Youkai Girl(SA) comes very close, though, followed hard upon by The Grimoire of Alice(MS).
Ending Theme: The Earth Spirits' Homecoming(SA). Peacefully wonderful.
Now for random stuff:
Best Marisa Theme: Screw LCMS, this one goes to
The Witches' Ball ~ Magus, Marisa's theme from Shuuso Gyoku.
Best Reimu Theme: I'm incredibly partial to Maiden's Capriccio ~ Dream Battle(IN), though Dichromatic Butterfly ~ Ancients (also Shuuso Gyoku) is REALLY close.
Best PoDD Theme: Strawberry Crisis!! Though Maniacal Princess and Vanishing Dream are both very high up there.
Best PoFV Theme: I'm'a gonna have to go with Flower Land. I don't care for Yuka's LLS tracks, but I really have gotten to love Flower Land.
Feel free to create more categories, or respond to the ones I put up, or both!