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[b]Title Theme - Sealed Gods (MoF)[/b]
I literally don't even have to think about this one-it's the only title theme song (except maybe Newshound from DS, but even then not really) that I've gone out of my way to listen to.  I really like how ZUN did his own thing with it while still mixing in the traditional title theme melody, and also mixed in the water sounds.
[b]Stage 1 Theme - The Refrain of the Lovely Great War (GFW)[/b]
This was a tough pick between this as The Dark Blowhole (SA).  But in the end, the song that sets the tone for the rest of the game better prevailed.  This is the song you hear the most, by far when grinding, and GFW earns extra points by having never once gotten stale during a grind session-SA did a couple times during the 100 restarts it took me to not die before Green Eyed Jealousy.
[b]Stage 1 Boss Theme - Stirring an Autumn Moon ~ Mooned Insect (IN)[/b]
If you asked me a couple years ago, I'd have given this to Princess Inada is Scolding Me in an instant.  But now, I've had a lot more time to listen to these and I can really appreciate this song-the way it loops is very nice, and it manages to feel both slightly imposing and like a Stage 1 boss theme at the same time.  I have nothing bad to say about this one.
[b]Stage 2 Theme - Humans and Youkai Coming and Going at the Canal (DDC)[/b]
For a moment I was putting Welcome to Youkai Temple (TD) here...but then I remember that this song was pure awesome.  DDC as a whole really nailed the soundtrack outside of Stage 1 for me.  This is the Stage 2 I've played the least, but the song was still more than memorable enough to evoke memories of what happens in the stage at various points in the song.
[b]Stage 2 Boss Theme - Dark Side of Fate (MoF) AND Dullahan Under the Willows (DDC)[/b]
I couldn't decide between these two from how fundamentally different they are.  Hina's theme is fast paced piano with a catchy melody, wihle Sekibanki's is much more melodic and almost rock-like with the electric guitar.  I listen to both while doing random things fairly often, and they're just too different for me to really pick a favorite.  I think I'd give the edge to Sekibanki's theme if I had to, but I honestly don't know.
[b]Stage 3 Theme - Walking the Streets of a Former Hell (SA)[/b]
Tough choice for Stage 2 boss?  Easy choice here.  I've always loved this theme and it's outright my favorite stage theme in the entire series.  Perfectly fitting for the approach to Yuugi, almost feeling like a party is about to start.  There's also just enough edge to the second half to let you know that something big is coming up, so don't let your guard down!  The loop is a bit abrupt, but I don't care it's just such an amazing song.
[b]Stage 3 Boss Theme - Plain Asia (IN)[/b]
I like piano.  The main melody is relaxing but still lets you know Keine is serious, the 'improv' parts are beautiful and again, I have nothing more to really say here.  It's been another long-time favorite for the spot, even back when I started 4 (wow, it's been that long...) years ago.
[b]Stage 4 Theme - Fall of Fall ~ Autumnal Waterfall (MoF)[/b]
Not many people seem to like this song, it seems.  I guess for being a favorite is has some incredibly stiff competition with The Capital City of Flowers in the Sky (which is alright but not my style), Retribution for the Imperishable Night (which is awesome but gets quite overshadowed in-game) and Interdimensional Voyage of a Ghostly Passenger Ship, which I nearly put here.  In the end though, I had to go with Fall of Fall.  It sounds amazing while the stage destroys you, what's not to like?  The part where Momiji comes in only serves to kick off the beat further, and if you let the song keep playing after Aya shows up...the tone shift and accompanying rhythms are really what MAKE this song be my favorite pick above everything else.
[b]Stage 4 Boss Theme - Phantom Ensemble (PCB) AND Captain Murasa (UFO)[/b]
Another set where I just couldn't decide.  Choosing one of these two would really mean choosing a metric to judge the songs by, either how well-suited they are for the character (in which case Phantom Ensemble takes the edge) or how often I go listen to it (Captain Murasa takes a very small edge there).  Either way, both really good songs, but like the Stage 2 boss theme, if I had to choose I think I'd pick the more modern one, but I can't say for sure.
[b]Stage 5 Theme - Rural Makai City Esoterica (UFO)[/b]
Yet another difficult pick, but in the end I decided based...on the midboss part.  When Sanae shows up, The Primal Scene of Japan the Girl Saw does shift, but it doesn't really do anything and then jumps straight back to what it was doing before she shows up.  It could be a plus, but to me it knocks it down a spot.  Tojiko does something similar, but the song keeps its original melody in the background-shame the original melody of The Great Dream Palace Mausoleum is a bit too soft and relaxing for my liking.  The closest anything came to beating this was The Shining Needle Castle Sinking in the Air, which is also relaxing, but then turns ominous.  Seija shows up and turns the song on its head (I made a bad pun. laugh.)  Still, the foreign energy and the tense encounter with Nazrin give this one to UFO.
[b]Stage 5 Boss Theme - Faith is for the Transient People (MoF)[/b]
Rocking.  Piano.  That is all.
[b]Final Stage Theme - Cemetery of Onbashira~ Grave of Being (MoF)[/b]
I'll be the first to admit this placement is based almost entirely on feelings and memories of tense runs.  But in the end, it was either this or Voyage 1969, and Grave of Being has more energy behind it, more emotions associated with it.  The final boss theme is going to be even more personally biased...
[b]Final Boss Theme - Border of Life (PCB) AND Gensokyo Millennium ~ History of the Moon (IN 6A) AND Flight of the Bamboo Cutter ~ Lunatic Princess (IN 6B) AND Fate of Sixty Years (PoFV) AND The Venerable Ancient Battlefield ~ Suwa Foughten Field (MoF) AND Solar Sect of Mystic Wisdom ~ Nuclear Fusion (SA) AND Emotional Skyscraper ~ Cosmic Mind (UFO) AND Shoutoku Legend ~ True Administrator (TD) AND Kobito of the Shining Needle ~ Little Princess (DDC)[/b]
Wait, you mean I can't just say most of them?  But they're all so good, and choosing one favorite would be entirely based on close runs I've had... I mean I guess I can try to choose one but this is by far the hardest choice of the bunch.  ...  Nope I lied I can't choose just one.
[b]Final Boss Theme - The Venerable Ancient Battlefield ~ Suwa Foughten Field (MoF) AND Emotional Skyscraper ~ Cosmic Mind (UFO)[/b].
Alright, the reasons for this aren't easy to explain, so if you don't care, skip ahead to the extra stages.
Still reading this?  Good.  I left out Septette because as good as it is as a song, it pales in comparison to, well, everything else for me.  I fully expect to be poked fun at for this (by one person in particular).  Close runs?  Not amount of intense runs would save this, though my first lunatic 1cc getting through the first bunch of the fight on just 3 bombs was a nice memory.  Border of Life was a no brainer placement, it's intense all on its own.  Due to Resurrection Butterfly following it up, even having resources left at the end keeps the intensity, making every run that isn't loaded close.  Suika's theme is skipped because lol fighting game.  Good song, but I don't have anything associated with it.  Gensokyo Millennium has my "never give up" run which was on the brink of death for the entire Eirin fight-seriously, 1 bomb going in, 1100 point items would be reached after Game of Rising...and I pulled through with that bomb being spent on Game of Rising itself, lose the life instantly, bomb, 2 bombs for Apollo 13 and then a clutch Astronomical Entombing capture...which a lot of dodges I shouldn't have gotten away with, as much as I felt like I literally could not fail.  -line break-
Lunatic Princess has no such connotation from close runs...oh wait, my failed lunatic no focus attempts that nearly succeeded had so few resources left for Kaguya, that even though they failed they stick out due to some insane captures.  My final clear started imploding on Kaguya resulting a close finish anyway...Fate of Sixty Years plays vs. a cheaty boss.  It's ALWAYS going to be intense, you're ALWAYS going to hear it for a long time, and it does a great job of not getting old and keeping its intensity even during the slow parts. (skip MoF for now).  Wonderful Heaven got ignored for the same reason as Suika's theme.  Nuclear Fusion is awesome on its own, but I have no clutch runs.  (skip UFO for now too)  True Administrator I really liked when I first heard it, but the nature of TD means you either win in a landslide, fail horribly or choke right at the end and have a close finish.  My first lunatic 1cc had 4 lives for Miko...and I imploded but squeaked out a 0/0 finish.  Good song, no memories.  Sukuna's theme is amazing as well but again, has nothing really backing it up other than a failed 1st lunatic attempt which capped the survival and Attack on Dwarf blind (for lunatic-I'd faced them on normal and hard, before) with nothing left.  Oh and I've never actually heard Kokoro's theme :V

The reason I have to put Kanako's and Byakuren's on top should be relatively clear from the trend-the close runs.  Suwa Foughten Field has this intensity about it that even when you're on top, guaranteed to meet your goal, it doesn't always feel like it.  The runs that cement this from being close?  Hard no bombs, MarisaC, 0 lives going into Kanako.  Perfect the fight.  Lunatic no bombs, 3 lives going in.  Anything can go wrong at any moment, clear with 0 lives left (3rd non, Source of Rains, VoWG).  Virtue of Wind God timeout.  Hard no vertical (nothing left at the end of VoWG).  Normal 120 FPS (nearly thrown away at the end, very intense).  So why is UFO's here if I haven't cleared its lunatic yet?  What close memories put it on top?  Truthfully, none but first clears of difficulties and the song itself.  It's grown on me quite a bit over the years, and it also feels...hopeful.  Perhaps it's anticipation for the UFO lunatic 1cc grind that I'll inevitably do eventually.  Perhaps not.  But those are my top final boss themes and my reasons, flawed though they may be, the song choices are still based on the song itself, with the feelings evoked being secondary.
[color=red][i]k, that wall is over...you can start reading again if you skipped all that[/i][/color]

[b]Extra Stage Theme - Last Remote (SA)[/b]
Feels like a leadup to an epic confrontation.  Honorable mention to Thunderclous of Magical Power, which narrowly lost the spot.
[b]Extra Boss Theme - Native Faith (MoF)[/b]
Anyone who knows me knows this one.  This song is the reason i started going for survival accomplishments.  This song is the reason I chose to play the way I did.  This was, and possibly still is, my absolute favorite Touhou song.  I set out to clear the stage for the first time over 3 and a half years ago.  I did.  I set out to do it no focus.  I did.  I set out to do it without bombs.  It was a struggle, aided along by a well timed challenge here, with 4 deaths.  I decided to perfect the stage.  It took me a month, but within 9 months of discovering Touhou I had perfected Mountain of Faith extra.  That decision is what set me down the survival challenge road.  All because this was my favorite Touhou song at the time.  It's impossible for me to not enjoy it, impossible to not look back and see where liking it has taken me.  Some people started because of U. N. Owen Was Her? (which I don't really like).  I started playing because the games were fun, kept playing because they were fun, and chose my path based on really liking this song.
Oh, and the reason I liked it then is due to how happy and upbeat it is, the fact that it's awesome piano, and Suwako is just playing with you.

If Native Faith was off the table I'd have to give this spot to Primordial Beat ~ Pristine Beat (DDC), but IN, SA and TD all come close to Raiko's theme.  It's just an absolute landslide victory for Native Faith though.
[b]Ending Theme - Leave Flowers in Fantasy (PoFV)[/b]
I listened through all of them to make sure, but this one is just my favorite.  Peaceful, its own thing, a fitting reward.  Shrine at the Foot of the Mountain (MoF) came close, but in the end there really was no option.  I can't completely describe why I prefer this one, all I can say is that I do.
[b]Credits Theme - The Gods Give Us Blessed Rain ~ Sylphid Dream (MoF)[/b]
Same as above, only the close call was Flower of Soul ~ Another Dream (PoFV).
[b]StB Theme - Sleepless Night of the Eastern Country[/b]
For one, I don't really like Retrospective Kyoto that much.  The second reason this is here is because I do like the original, it never got old while playing through StB.  The third reason is the only time a remix helped a placement here...[url=https://www.youtube.com/watch?v=BQiveMR9W98]Labyrinth of Touhou[/url] has this as its 2nd main battle theme.  Like the original, it never got old despite showing up right as you need to start grinding, a lot.
[b]DS Theme - Nemesis's Stronghold[/b]
Bell of Avici ~ Infinite Nightmare got old fast.  This...not so much.  Even before spending 5 hours (I was bad then and shouldn't have been trying to do it yet) clearing Vague Recollection of Kinkaku-ji I didn't really like Infinite Nightmare.  Nemesis's Stronghold I did always like, however.  Honorable mention to the song that plays when you unlock Hatate for being a remix of the title screen, which is a remix of the standard title theme remixed throughout the series.  It's different enough that it's practically its own thing, but Nemesis's Stronghold wins.
[b]Fan-made Theme - Life Guiding Song ~ Prospect Mirai (Mystical Power Plant extra boss) AND Rumble Temple (TD Phantasm boss)[/b]
Had to give these two at the very least an honorable mention-seriously, check these out if you haven't heard them.  Prospect Mirai is upbeat and incredibly catchy (like a pop song...only awesome instead of awful!), while Rumble Temple is incredibly energetic (and even has electric guitars in the background of piano, and then the piano shifts to the background and it's trumpets in front and then the electric guitars come back to the background and I've had this in the background for an hour without noticing that it'd been an hour).

PC-98: 0
EoSD: 0
PCB: 1
IaMP/SWR/HM: 0
IN: 2
PoFV: 1
MoF: 8
SA: 2
UFO: 3
GFW: 1
TD: 0
DDC: 2
ok that took forever to write, so long in fact that 4 people posted their lists (yes I started writing this up shortly after Mino's post)