How they fly...your version

[Vael]

I imagine Reimu either using the Border to allow her to ignore gravity in Gensokyo and then directing herself to a particular location or using one of the many sky/wind gods' powers to fly.

With Alice, I bet she holds herself up using her dolls.

There's a reason why Patchy's always holding a book, as her focus, she uses it to fly as well, but she's powerful enough to fly on her own...her body won't let her though.

Then there's Komachi, I bet she jumps, increases the distance between her and the ground, and then reduces the distance between her and a particular spot...then again, she could just walk there as well.

I sometimes imagine Youmu pulling a Son Goku and getting carried to her destination by Myon. If she's in a rush, I bet she could just run where she needs to go.

Meiling...I bet the reason why she sucks at Danmaku is because she's manipulating the chi around her to 'fly' or in this case, to lift her up and move her about like telekinesis.

Sakuya, maybe she doesn't fly altogether, she slows down Time for herself (making her look fast and to make sure others don't see what she's doing and how), jumps into the air and stops the time directly under her feet, making a platform of sorts, and then leaps from 'platform' to 'platform'. Or she could just stop time, stroll over to her destination, and then release it for that vanishing maid act.

Kaguya can't fly, it just takes her forever to fall even a millimeter, enough for her to walk in the air from place to another.

Eirin made a drug that allows her to fly, Reisen has learned how to make this drug. It's an extremely unique drug, suited only for one user, hence all the past experimentation.

Yuuka? She channels her power through her parasol like a Magician would their focus, not very efficient, rather slow, but she doesn't care.

============

That's it for now, I'll be back when I come up with more ideas.

[Starxsword]

Reisen has learned how to make this drug. It's an extremely unique drug, suited only for one user, hence all the past experimentation.

Aw, I thought you were going to say Reisen makes everyone and herself THINK that she is flying.
If you think it, it will happen.

[MMX]

Well Speaking of  Ten Desires characters:

Kyouko flies by rapid flipping of her ears,
Yoshika is just a freaking zombie out of nowhere, so why not,
Seiga uses the power of Tao to attain levitation,
Futo is onna boat!
Mamizou... Well i dunno. Maybe by her tail or something,
And Miko has so fabulous power to listen to ten people at the same time, that such an easy thing like flying is not a problem at all

[Ibaraki Ibuki]

I think it's simpler to assume everyone can fly because they believe they can touch the sky. (And they think about it every night and day, to the point where they can spread their wings and fly away.) 

also,

Kyouko flies by rapid flipping of her ears

maybe her ears are detachable like Chiyo-chan's pigtails?

[Kaisou]

Everyone's clothes are a certain brand that makes them fly. If they wear some cheap knock-off then they'll jump up and fall back down shortly after. Where they get their clothes? I bet Yukari switches the flightless ones with the brand while they're sleeping. Speaking of which, Yukari is a special case because she's manipulating the border of standing and flying of something to make her levitate.

[Yadogari]

They are very quietly saying to themselves "You just gotta believe!"




Or they get Colonoscopies very, very often.

[Irate Researchers]

It's Spiral Power.

[draganuv15]

Well Sanae flies like Superman so we can rule her out.

Everyone just has infinite double-jump

[Wolfishly]

Ran uses her copious amount of tails like a helicopter and thus propels herself through the air.
Miko uses her wing-hair and saintly powers.

[Vael]

It's Spiral Power.

Wait one minute here...Sanae's power is create Miracles. Spiral Power also does that.

Sanae says that common sense does not apply to Gensokyo. Spiral Power is wielded to drill through the heavens and kick impossible to the curb.

Does Sanae have Spiral Power helping her fly?

[circle nine]

Everyone's clothes are a certain brand that makes them fly. If they wear some cheap knock-off then they'll jump up and fall back down shortly after. Where they get their clothes? I bet Yukari switches the flightless ones with the brand while they're sleeping. Speaking of which, Yukari is a special case because she's manipulating the border of standing and flying of something to make her levitate.

I was thinking something similar actually, but more along the lines of 'enchanted' clothing (Morrowind's levitate?), for any character that doesn't have any other method of flying (eg: Sakuya).  This can also, to a lesser extent apply to items (eg: Marisa's broom, though she didn't need it in FW).  Enchanting clothes for flying is a fairly difficult process however, hence why nearly everyone in Gensokyo wears the same outfit in every single game .

[Tempest]

Given how natural flying seems to be, if it's not through some other obvious means (wings, Marisa's magic broom...) or otherwise explainable method (Reimu's spiritual powers...), I would guess flying is a dormant ability in all of Gensokyo's residents. Without making it sound too much like that certain other overly known franchise whose name starts by a D, the ki explanation sounds like the most natural given the nature of the realm. Magic seems to be at the base of mostly everything in Gensokyo, and surely magic is manifested through personal power, or capability. Ki is one name of this power.

To be fair, I wouldn't be surprised if flying is among the easiest of abilities to master. I know that common sense is not required in Gensokyo.

[KLH]

Given how natural flying seems to be, if it's not through some other obvious means (wings, Marisa's magic broom...) or otherwise explainable method (Reimu's spiritual powers...), I would guess flying is a dormant ability in all of Gensokyo's residents. Without making it sound too much like that certain other overly known franchise whose name starts by a D, the ki explanation sounds like the most natural given the nature of the realm. Magic seems to be at the base of mostly everything in Gensokyo, and surely magic is manifested through personal power, or capability. Ki is one name of this power.

To be fair, I wouldn't be surprised if flying is among the easiest of abilities to master. I know that common sense is not required in Gensokyo.

Wow. That is the best and most reasonable explanation I've seen thus far.
(BTW i honestly don't know what that "d" franchise is)

[Starxsword]

I assume it is Dragon Ball Z.