The top 10 that I like at the moment:
10.
PCB 5 stage (
Youmu) -
Eastern Mystical Dream ~ Ancient Temple------- Despite the excited beats, there is a certain mystic feeling to the song, especially the ghastly echoes in the background, that draws me towards it. (Just a note, PCB stage 3's music isn't bad, but is really out of place with the overall tune of the other stages. Grrr.)
9.
MoF 4 stage (
Momiji) -
Fall of Fall ~ Autumnal Waterfall------- Very lively and nature-like, and certainly fits very well in the game with the waterfall in the background.
8.
SA 3 stage (
Yuugi) -
Walking the Streets of Former Hell------- Distinctly reminds me of a night market in a small town, with a festive atmosphere, beautifully portrayed by the pantatonic melody line. Also first song I listened beyond the character theme songs from Bad Apple.
7.
MoF EX stage (
Kanako) -
Tomorrow will be special, Yesterday was not------- While not exactly sounding festive, the song still has a curious divine tune in the harmony, and somehow portrays an image of Sanae sweeping the shrine grounds on a windy late-autumn morning.
6.
SA 5 stage (
Orin) -
Lullaby of Deserted Hell------- The tune carries a rather lonely and (somewhat) sorrowful feeling, under which (the harmony) appears surprisingly calm, without blaringly loud instruments on the melody. Somewhat a tender rendition of Orin's inner self.
5.
IaMP title -
Memory of Forgathering Dream------- Main menu theme of Suika's game, which I first came across while watching a MMD video on a lonely Alice befriending Suika. This association aside, its oriental tune is reminiscent of Ancient Temple, but more emotional, perhaps portraying a more sober Suika yearning to rediscover herself after her banishment from the Youkai Mountain, before meeting Reimu.
4.
TD 5 stage (
Tojiko) -
The Hall of Dreams' Great Mausoleum------- The tune portrays a grandeur feeling from the very beginning, illustrating the entrance hall of the mausoleum and its wonders, almost inviting the player to carry on listening/playing to find out more.
3.
MoF 6 boss (
Kanako) -
The Venerable Ancient Battlefield------- A grand show of the awe-inspiring majesty and power of Kanako over the mountain, especially in the transition from triple-time to quadruple time (with the broken octave chords) and the second verse (with the vocals). Distinct wind- and nature- sounding tune, similar to most of the later boss themes in MoF.
2.
EoSD 6 boss (
Remilia) -
Septette for the Dead Princess------- The first Touhou theme music that I came upon. The boss theme of the first Windows game echoes the personality of the vampire mistress -- powerful, proud, somewhat sinister, and (after the cadence change) a little playful and relationship-seeking. However, the overall melody is still prominent and consistent, suggesting her firm and collected nature. Till date, Remilia remains one of my favourite characters.
1.
HM boss (
Kokoro) -
The Lost Emotion ------- The song has a gradual buildup in intensity from the beginning, with angry sounding organ chords in the background, akin to that of frustration and madness in Kokoro while she battles the player. After a while, a cold-sounding intermezzo of acoustic and piano takes over a while, where the storm seems to go into the background and the intense battles both outside and inside Kokoro come to a standstill, almost as if she has gotten a hold of her own feelings, before the intensity returns again as Kokoro reminds the player that she is not finished. My fondness for this music has caused it to instinctively appear during confrontational chapters in literature.
Credits to User: Fightest, for explaining a lot of the characteristics of the boss themes
here. I'm just tweaking some of his inferences for my own interpretation.
These are favourites
as of July 2014; may change over time.
Some of the more famous boss themes are nice, but they're just not at the top of my list.
