Favorite song for each game?

You're missing so many games it's not even funny:

HRtP: Magic Mirror
SoEW: Complete Darkness
PoDD: Tabula Rasa ~ the Empty Girl / Vanishing Dream ~ Lost Dream
LLS: Scarlet Symphony ~ Scarlet Phenome / Spirit Battle ~ Perdition Crisis
MS: Plastic Mind
EoSD: U.N Owen was Her?
PCB: The Capital City of Flowers in the Sky
IaMP: Intermezzo / Scarlet Night
IN: Retribution for the Eternal Night ~ Imperishable Night
PoFV: Poison Body ~ Forsaken Doll
StB: Sleepless Night of the Eastern Country
MoF: The Gensokyo the Gods Loved
SWR: Bhava-agra as Seen Through a Child's Mind
SA: Last Remote / Lullaby of Deserted Hell
UFO: Fires of Hokkai
Soku: The Scenery of Living Dolls
DS: Bell of Avici ~ Infinite Nightmare
GFW: Can I just stick with "the whole soundtrack"?
TD: Youkai Girl at the Gate
HM: The Lost Emotion
DDC: Inchlings of the Shining Needle ~ Little Princess
ISC: Romantic Escape Flight
ULiL: way too many. let's just stick with Last Occultism ~ Esotericist of the Present World
LoLK: Clown of the Star-Spangled Banner / Pure Furies ~ Whereabouts of the Heart

HRtP: Magic Mirror
SoEW: Complete Darkness (favourite PC98)
PoDD: Strawberry Crisis
LLS: Inanimate Dream
MS: Grimoire of Alice
EoSD: Septette for the Dead Princess
PCB: Necro-Fantasy
IaMP: Missing Power
IN: Lunatic Princess. Best song in Touhou. Peroid.
PoFV: Riverside View
StB: Sleepness Night of the Eastern Country
MoF: Suwa Foughten Field
SWR: Wonderful Heaven
SA: Hartmann's Youkai Girl
UFO: Heian Alien
Soku: Idk, let's just say Okuu's arrangement
DS: Infinite Nightmare
GFW: Magus Night
TD: True Administrator
HM: Lost Emotion
DDC: Shining Needle Sinking Through the Air (favourite stage theme)
ISC: Eternal Transient Reign
ULiL: Battle Field of Hanahazama (prob spelt wrong lol)
LoLK: Eternal Spring Dream

HRtP: Magic Mirror - The beta version of Complete Darkness, this is likely the only song in HRtP that I like all the way through. Most of them start off great, although eventually I get tired of the repetition and the silly endings to each theme.

SoEW: Complete Darkness - SoEW's soundtrack is pretty shit overall, so this and the stage 1 theme are the only two highlights IMO. It's a good song in its own right, but it really shines in arranges, ending up being one what I feel is one of the best PC-98 tracks.

PoDD: Maple Dream... - This song isn't actually amazing if you sit down and try and rationally compare it with other ones, but it was one of the first PC-98 songs I heard and it was quick to be one of my favourites. I think it's a case of nostalgia more than anything xD. I actually like the CoSD version better.

LLS: Faint Dream ~ Inanimate Dream (Unused Version) - Great pace and very fitting of Yuuka after she is fully prepared to fight. LLS has some other great songs too, and if I wasn't including unused tracks I would probably pick Reimu, Marisa, or Elly's themes or something. The unused Inanimate Dream isn't as annoyingly repetitive as the original, though, so it becomes a song I like quite a bit.

MS: Peaceful Romancer - I really like the fast pace of this ending theme, as well as the slides, although towards the very end it does get a bit high-pitched. Either way, I think it's a very fitting song for effectively the last thing heard in Touhou before the windows era, and at the time ZUN may not have known he was going to come back to it, so it is a true send-off. I would have picked Shinki's theme above this, although I feel that Shinki's theme sounds worse when arranged so it's difficult to rate so highly a song that only sounds good in one rendition.

EoSD: The Centennial Festival for Magical Girls - About 1:35 onwards I get goosebumps. I had a hard time picking between this, Voile, Remi's theme and Flan's theme, but I think this theme doesn't sound quite as MIDI as the other three and I love its bass, so I had to choose it in the end.

PCB: Ghostly Band ~ Phantom Ensemble - PCB has a pretty all-round good soundtrack, this theme is the most concise of them though, and it's the only thing that stops me from writing off the Prismrivers as shit-tier characters.

IN: Flight of the Bamboo Cutter ~ Lunatic Princess - The arpeggios in this are way better than Mokou's theme's runs IMO. I've always thought that IN has the best instruments ZUN has ever used, and I feel that this theme epitomises them into a song that feels powerful, not epic, but elegant, and is far superior to the character it's attached to.

PoFV: Touhou Judgement in the Sixtieth Year ~ Fate of Sixty Years - When I first listened to this, it wasn't in PoFV, and I kinda thought that the song just dragged on and on and wasn't really that good. Once you actually fight Eiki though, I feel that it's the perfect song for the fight, and captures the kind of feeling that PoFV is meant to give off, IMO. Not to mention that it kicks in at just the right time during Yuuka's conversation with Eiki to make it probably my favourite final boss fight in terms of atmosphere.

MoF: Cemetary of Onbashira ~ Grave of Being - Almost chose the EX stage theme over this, but listening again, this really is a hype theme when you're off to face a Goddess (and the EX stage theme is a bit too repetitive).

SA: Corpse Voyage ~ Be of Good Cheer! - Like Shinki's theme, I feel that no arrange of it is very good, but unlike Shinki's theme I feel that this is because the original is composed so well (rather than happening to sound good with the instruments chosen), and is therefore worthy of best SA theme. It's really fun, fast-paced, full of energy, and fits the character perfectly.

UFO: Interdimensional Voyage of a Ghostly Passenger Ship - UFO overall has a fairly decent set of themes, although I really like the quirkyness of this one, and I think it gives the stage a comfy feel rather than the 'drifting' feel that all the other stage themes give to me. That's not to say I don't like them, but this is just more fun to listen to outside of the game.

GFW: The Great Fairy Wars ~ Fairy Wars - I love all of GFW's soundtrack, so this was a very difficult choice. Went with this over the title theme because it is much longer than the title theme.

TD: Night Sakura of Dead Spirits - It's kinda sad that I think the best song in TD is the stage 1 theme. I think it's really deep and nice sounding, makes such a long boring stage tolerable. Mamizou's theme is nice too, although the bass in it is a bit too much I think.

DDC: Thunderclouds of Magical Power - Not as nice sounding as the stage 5 theme, but way more atmospheric and the choir and brass is just awesome. The stage is also way more fun.

LoLK: Faraway Voyage of 380,000 Kilometres - A contender for favourite stage theme. I think it starts off with a lot of atmosphere that really fits what I see space and the moon as, and then in the latter half becomes so epic that it's almost a shame the stage isn't amazingly fun.

HRtP: Eternal Shrine Maiden - I don't play this game, but god this song makes me want to cry when I listen to it. You can sense the sorrow in this song. It just gives off the vibe of "this is where the series began" (although technically the title theme was the first song). It also gives the impression that Reimu is weak and still growing, which is true as she can't fly and has to hit her ying yang ball to make it attack.

SoEW: Hakurei Shrine ~ Eastern Wind - This song also makes me want to cry for some reason. What is it with ZUN and melancholic stage 1 themes in these early games?

PoDD: Strawberry Crisis - Badass theme. Probably my favorite PC-98 theme. This game, although rarely played by me, is my favorite PC-98 game also.

LLS: Faint Dream ~ Inanimate Dream - This is a pretty epic final boss theme. I love how it's not too tense but still serious at the same time. Yuuka is one playful fellow.

MS: Alice in Wonderland - Such a royal and dreamy song~ I love the general atmosphere in this stage as well.

EoSD: Locked Girl ~ The Girl's Secret Room - This song has sentimental value to me as Patchouli used to be one of my favorite characters back in the day. I love how melancholic this theme is. Fitting theme for an introverted hikikomori just like me!

PCB: A Maiden's Illusionary Funeral ~ Necro-Fantasy - Yukari's theme used to be my favorite, until I set it as my ringtone. After hearing that song everytime someone called me from work, I now get triggered everytime I hear Necrofantasia. Luckily, Ran's theme doesn't have the same start as Yukari's theme, so I can still enjoy the lovely main melody that these themes share.

IN: Cinderella Cage ~ Kagome-Kagome - I love the kagome-kagome melody inserted in this song. I also love how it dramatically picks up the pace after the introduction. This song is just overall very melancholic and just beautiful.

PoFV: Fate of Sixty Years - I love how tense this song is. And it doesn't even get soft at all. It's such an adamantly tense song for such a chaotic fight. Very fitting IMO!

MoF: The Japanese Wilderness the Girl Watched - Beautiful and oriental, and also very dramatic. I love the contrast this song has with the stage 4 theme. It gives off that "you're approaching the end of the game" feel that I really like.

SA: Heartfelt Fancy - This song has that airy and dramatic feel to it, but I also feel like it gives me hope in a way. It's also really quirky at some points which I really like. It really fits the atmosphere of this stage! What is it with me liking dramatic and sorrowful songs? Lol.

UFO: At the End of Spring - The piano at the beginning is soooo beautiful and leaves an amazing first impression on the game! The whole song makes me want to just jump out my window and fly into the skies!

GFW: Great Fairy Wars ~ Fairy Wars - Amazing song for the final boss. It's so playful but fast paced at the same time, making it still tense but lighthearted. It goes well with the atmosphere of this game! Also that flute melody is beautiful ;_;

TD: Futatsuiwa from Sado - I love how catchy and playful this song is! It also has that nice oriental foreign hipster feel to it. Fitting for Mamizou! It's also cool how much this song contrasts the rest of the game.

DDC: Kobito of the Shining Needle ~ Little Princess - This game has so many good songs, it's really hard to choose. But this song is by far my favorite final boss theme. It's got everything you want in a final boss theme. The tense beginning is awesome and then the main melody is among my favorite melodies in Touhou. The badass and beautiful piano is an amazing thing to have in the background as well. God this song is so beautiful and dramatic. It really makes you feel like Shinmyoumaru isn't the bad guy after all, but just deceived.

LoLK: The Sea Where One's Home Planet Reflects - Beautiful. Simply beautiful. The soft melody that plays throughout this song is just so beautifully made and just makes me want to seriously cry. It feels almost, lonely, but gives that feeling that you're really far away from home. When the flute comes in, you get this heroic vibe that makes you feel like the world's fate is in your hands.

it means that lunatic princess is a top tier song and kaguya isn't a top tier character.

i have mixed opinions on this statement

HRtP - Strange Oriental Discourse
SoEW - Wizard Yuuka's theme
PoDD - Yumemi's theme
LLS - Sleeping Terror (stage 5 Yuuka)
MS - Mai's theme
EoSD - Stage 4 music
PCB - Alice's theme
IaMP - Title screen music (Maybe, IaMP is hard to pick from)
IN - Stage 2 music
PoFV - Shiki's theme
StB - Title screen music
MoF - Stage 5 music
SWR - Remilia's theme
SA - Extra stage music
UFO - Stage 5 music
DS - Infinite Nightmare
Soku - This one
FW - 3 fairies theme
TD - Yoshika's theme
DDC - Awoo's theme
ISC - Title screen music
LoLK - Murrica's theme
HM/ULiL - These games don't exist
Riverbed Soul Saver - Momohime's theme
Mystical Power Plant - Riko's theme
Takkoman - Channel Seaside
The Last Comer - Stage 4 music
Never Extinguished Flame - Shuzo's theme
Resurrection of Heaven's Liquor - Suika's theme
THF230.zip - Stage 6 music
Juuni Jumon - Amaya's theme

I think I got most of them anyway.

EoSD: Patchouli's theme - This particular arrange made it my favorite because it makes her sound like a final boss and back in the day she actually was the final boss as I would always game over on her, it brings good memories
PCB: Stage 4 - There's a lot to be said about a song that makes an otherwise unbearably long stage a very enjoyable one
IN: Kaguya's theme - it's the one reason I enjoy fighting her more than Eirin
PoFV: Eiki's theme - it's probably the best final boss theme ZUN has ever composed
MoF: Stage 4 - too bad the stage ends before the song does
SA: Stage 5 - This is one of the best pieces of music I've ever heard
UFO: Stage 1 - it's funny, the girls are flying all the time, but this is the only theme that makes you feel like you're actually doing it
TD: Stage 4 - really fits the "accelerate" thing of the stage
DDC: Stage 5 - it's just a chill song
LoLK: Stage 5 - The song and actual stage are paced together perfectly