Well shit, now I gonna spend like an hour or two writing this. Thanks, mino! (I'm just kidding I love ya) Incoming wall of text btw.
Anyway I'm going to try and avoid just saying SA (because it is the best soundtrack, again kidding) for all my favorites so I'll probably be naming 2 for any that have SA in it. Otherwise, it would pretty much just be SA throughout. And that would be boring.
FavoriteTitle: Mysterious Purification Rod (DDC)
I don't know, there's just something about this title theme that I really like. I think it's just the calmness of it. I really like A Shadow in the Blue Sky (UFO) as well, but DDC just barely wins out.
Stage 1: The Dark Blowhole (SA)
Yeah, I'm not super big on most the stage 1 themes, so only SA's gets on here. I really, really like the piano in this song and how it sound effect matches with the rocks falling on the screen. Music matching action on the stage is a big draw to a lot of songs for me.
Stage 1 Boss: She's in a temper!! (SoEW)
Like stage 1 themes, I'm not too big on stage 1 boss themes as well, but I really do like SoEW's. Personally, I think it sounds better than Rika's EX theme. Not too much to say really, I just like this song.
Stage 2: The Bridge People No Longer Cross (SA) AND Humans and Youkai Coming and Going at the Canal (DDC)
I love those marimbas in SA's. It just sounds sooooo good. As for DDC's, oh god that piano I just love it so much. Even the ZUNpets sound better than usual in this song. The composition in both of these are so good. Also, long titles are long.
Stage 2 Boss: Green-Eyed Jealousy (SA) AND Youkai Girl at the Gate (TD)
For SA's - Again, dat piano. It sounds so sad at the start and then it builds, I love it so. As for TD's, I do actually like a lot of tracks from TD, but most of them just fall short of other themes in the series, this one is not the case for me. I love the echo-y sound in this song and it fits so well with the fight. The flute is so perfect in this song and just fits so well with the strange instrumentation and helps keep the song coherent.
Stage 3: Romantic Children (MS) AND The Gensokyo the Gods Loved (MoF)
I swear, MS is the PC-98 SA of my music choices sometimes. I really don't know why I love this song so much. The pacing is just so good, the instrumentation is so good, the composition is so good. I pretty much love everything about it. Pretty much the same thing can be said about MoF's. I love everything about it.
Stage 3 Boss: Akutagawa Ryuunosuke's Kappa ~ Candid Friend (MoF)
Aaaaaaa I love this song so, so much. Sorry, sorry I just really like this song. It's a shame that you will most likely not hear the whole thing while playing. Doesn't stop me from reading the dialogue really slowly so I can listen to all of it. The song just sounds so moving I can not help but sing along with it.
Stage 4: Heartfelt Fancy (SA) AND Alice Maestra (LLS)
Heartfelt Fancy is Heartfelt Fancy. I cannot not love it. LLS was an instant like. Seriously, this song needs more attention. It is easily a major contender for my favorite PC-98 song. Too bad it's a bit short, ah well.
Stage 4 Boss: Satori Maiden ~ 3rd eye (SA) AND Illusionary Joururi (DDC)
SA's is just so perfect. It really does make me think that I'm fighting some weird monster and the fight just gets more and more surreal as time goes on. DDC's is just, just I don't know but I love the instrumentation. The really hard strums of the biwa(?) just sounds so strange on the ears that I kinda love it.
Stage 5: Lullaby of Deserted Hell (SA) AND The Shining Needle Castle Sinking in the Air (DDC)
SA's was one of my all time favorite Touhou songs, until DDC's happened and now I can't decide on which one I like more. Nothing really to say about either of these, I just love them. Ever noticed that like every other stage 5 theme in touhou is a very soft sounding song?
Stage 5 Boss: Reverse Ideology (DDC)
God dammit, Seija. I just really, really like this song. I know a lot of people hate Seija's fight so much, but I just can't because of her theme. The icing on the cake is that parts of it sound the same backwards (
here give it a listen if you haven't heard it before). Not sure if it was intentional or not.
Final Stage: Hellfire Mantle (SA)
Like stage 1 themes, Final stage themes just always seem kinda "eh" to me. I guess it's because they aren't particularly long so it is kinda hard to gauge the song. SA's is just one that I like. Sounds nice and dramatic. MoF's is OK too, I guess.
Final Boss: Solar Sect of Mystic Wisdom ~ Nuclear Fusion (SA) AND Shoutoku Legend ~ True Administrator (TD)
If you didn't see me picking Okuu's theme, then you didn't read the rest of the list. :V But seriously, it's just so powerful and yeah it sounds more final bossy than the other themes, but I don't see that as a bad thing. It just works so well with the fight. Same can be said about Miko's theme. It just sounds so powerful. The rising action of it is just so wonderful. It is the best song in TD in my opinion.
EX Stage: UFO Romance in the Night Sky (UFO)
Ha! You probably thought I was gonna pick SA's, well that's the runner-up. UFO's is just a song that struck a chord with me and never let go. I love the little laughs in it.
EX Boss: [obligatory] Hartmann's Youkai Girl (SA) AND Primordial Beat ~ Pristine Beat (DDC)
Koishi's theme is awesome. I can't say anything else about it that no one else probably hasn't already said. Raiko's theme seems to be less loved than the other extra boss themes. I love it on the other hand. Like pianos, I love drums and the drum solo in this song is so good. I'm so glad ZUN put in instruments other than just drums, the ZUNpets and piano add quiet a lot to it.
Credits Theme: Shrine at the Foot of the Mountain (MoF)
No real preference on the any of the credits theme; but if I had to choose a best, this one would be it. That guitar, mmmm.
Ending Theme: Returning Home From the Sky ~ Sky Dream (UFO)
I know it's just a remix of Byakuren's theme, but it sounds so lovely.
Fighting Games: This Dull World's Unchanging Pessimism & Shinkirou Orchestra [HM], The Lost Emotion [HM], Did You See that Shadow? [Soku/UNL], Flawless Clothing of the Celestials [SWR]
Other Side Games: Magus Night (GFW), Bell of Avici ~ Infinite Nightmare (DS), Midnight Spell Card -or- Eternal Transient Reign (ISC) Can't decide
Least Favorite I'm going to try and keep this shorter. -laughs-
Title: Spirit of Avarice (TD)
Eeeeeh, I just don't enjoy the instrumentation of this song. Mainly the beginning ruins the rest of the song for me. IN's opening is pretty up there too.
Stage 1: A Soul as Red as a Ground Cherry (EoSD)
Again, instrumentation.
Stage 1 Boss: Stirring an Autumn Moon ~ Mooned Insect (IN)
Don't hate, but I just don't like. As I said, I'm pretty neutral on most stage 1 stuff.
Stage 2: Lunate Elf (EoSD)
No comment.
Stage 2 Boss: Scarlet Symphony ~ Scarlet Phoneme (LLS)
Kinda boring really.
Stage 3: Nostalgic Blood of the East ~ Old World (IN)
Just never really liked it.
Stage 3 Boss: The Traditional Old Man and the Stylish Girl (UFO)
Pretty much the only song in UFO that I don't like. It just, doesn't feel right (the HM version is pretty good though).
Stage 4: Retribution for the Eternal Night ~ Imperishable Night (IN)
I just...don't know. I guess because I didn't really enjoy the opening theme I don't really enjoy this song either. I like parts, but for some reason it just doesn't click with me. Ugh, so frustrating.
Stage 4 Boss: Maiden's Capriccio ~ Dream Battle (IN)
Again, instrumentation. Doesn't sound very good on my ears as well.
Stage 5: The Primal Scene of Japan the Girl Saw (MoF)
This song is so frustrating. I love parts of it, but dislike other parts. There really isn't a stage 5 theme that I hate (except maybe IN's but that's still up for debate), so this one was kind of the default. Sorry, MoF.
Stage 5 Boss: Hiroari Shoots a Strange Bird ~ Till When (PCB) AND Legend of the Great Gods (TD)
PCB - Too high pitched for me to really enjoy.
TD - Takes too long to get going. I like it when it finally does...at about a minute into the song.
Final Stage: Starry Sky of Small Desires (TD)
Boring...
Final Boss: Septette for the Dead Princess (EoSD)
I'm sorry. I'm sorry. I'm sorry. I'm sorry. I just do not like this song very much. It's not a bad so, per say, but I just do not enjoy it.
EX Stage: Thunderclouds of Magical Power (DDC)
Don't hate, but it's just not as good as the other extra stage themes.
EX Boss: A Maiden's Illusionary Funeral ~ Necro-Fantasy (PCB)
Like the composition, but don't like the instrumentation.
Wow, that was a thing.
tl;dr I like SA and not so much IN.