I know I already listed SA as my overall favorite, but seeing all these lists makes me want to sort my fav's out too. Only EoSD, PCB, IN, MoF, and SA apply.
-Stage 1: SA. Upbeat and has a good melody. A great way to start out the game.
-Stage 1 Boss: Tie between Letty's and Yamame's themes. Seems like all S1B themes fall around the average mark (or lower), and these two are close enough to consider equal.
-Stage 2: SA. The beat is catchy as hell, and matches the cave-atmosphere of Stage 2 to boot.
-Stage 2 Boss: UFO. Okay, I lied. I don't have UFO, but I've heard Kogasa's theme, and it's amazing. HM to Parsee's theme.
-Stage 3: MoF. Such a beautiful piece, no wonder we see it ranked so highly among fan polls.
-Stage 3 Boss: EoSD. Despite the game's bad instrumentation, it doesn't appear as much of a curse here, letting me get through to the nifty melody.
-Stage 4: SA. Another beautiful piece, and it progresses quite nicely throughout the stage, adding to its awesomeness.
-Stage 4 Boss: SA. The melody, the presentation, so good... *falls over*
-Stage 5: SA. I know it contrasts with the style of other Stage 5 themes, but that's partly what makes it good (obviously has a touching melody to back it up). Even more evidence of how atmospheric this game's music is, especially considering its near flawless progression across the level.
-Stage 5 Boss: IN. S5B themes don't tend to be excellent either, huh? Reisen's theme is pretty cool for what it's worth, though.
-Stage 6: SA. The only memorable S6 theme, if you ask me. All the others are too short (probably because ZUN knew he'd be composing them for short stages) and thus don't have much to give.
-Stage 6 Boss: SA. As if there was any competition for this spot. A song that practically screams "final boss" in its deliverance, and totally appropriate for Touhou's first true villain.
-Extra Stage: MoF. Yet another beautiful melody, with a Japanese flair to it. HM to Last Remote, which comes really close here.
-Extra Stage Boss: PCB (Extra). Necro-fantasy's main melody (you know, the trumpet) is GODLY. You may not like how high it goes (as ZUN's trumpets tend to do), but for some reason I think the high pitch suits a theme for a fox quite well. Oh, and HM to Koishi's theme for it's "disturbing" tone (matches the nature of Koishi's ability).
See? SA is too good. :V