I'll do two lists: One that includes songs from the various fangames, which would alter it slightly, and one with ZUN-made games only.
First up, fangames included.
#5: Sky Filling Departed Spirit ~ Lightning World
It's energetic, yet strangely graceful at the same time. It has a modern yet.... oddly nostalgic feeling to it, which suits Matama and her look. Once again, amazing song and amazing fight. Also, dem trumpets.
#4: Fantasy Nation Daybreak ~ Player Prayer
Once again, a beautiful, graceful theme. It also conveys the benevolence I see in Momohime's character - she only wants to be with her family, and so this isn't a super-charged theme like, say, Nuclear Fusion. It works better, in my opinion.
#3: Emotional Skyscraper ~ Cosmic Mind
Truly, this is a dramatic battle. A battle between two wills, and conflicting world-views, and this song captures that perfectly. It's beautiful, amazingly so. There is no malice in this theme, either, and no side really wants to fight. One big reason I've always loved the songs in these games is how well they fit what they're playing too, and there is no better example then this song.
#2: Below a Deep Vanishing Cloud ~ Mow Down!, and A Single Glimmer
How ironic. From a purely technical standpoint, this isn't even really a fangame - though it has enough of the game's conventions I consider it so. Despite this, it deserves the spot. Part of it is the music - most of the songs from the Len'en series aren't that great, but this is amazing. It's incredibly epic and grand, yet emotional, which makes sense when you consider the 'incident' in the background and the story with Yarochi's brother/sister. I don't really know why I like this so much, but JynX went overboard with this :V
#1: A name cast off from the edge
This is the best fight from a fan game, period. It's creative, the music is awesome, and many of the patterns are cool. It certainty carries that 'she just stole your soul, hurrdurr' sense of urgency, yet certain parts have an elegance in it that I imagine as part of her character. It's also overwhelming, in a way similar to, say, Nuclear Fusion. Either way, this is an awesome song.
And now, the list from the official games.
#5: Swordsman of a Distant Star
Konngara's theme, and the best of the PC-98 songs by far.
#4: Shoutoku Legend ~ True Administrator
I've always loved Miko, she's one of my favorite characters. And the song simply suits her so well.
#3: The Venerable Ancient Battlefield ~ Suwa Foughten Field
This song is essentially dominance and power given form. That's somewhat of a theme throughout the fight, and in Kanako herself - complete power, confidence, and dominance over her opponent. It's sufficiently godly, too. It does what Nuclear fusion does, but.... better.
#2 Septette for the Dead Princess
Such an amazing song. It exudes grace and power, yet the song fits the rest of the character completely. Amazing song for an amazing fight.
#1 Emotional Skyscraper ~ Cosmic Mind
See above. Also, I've nearly spelled it 'spyscraper' three times now. Heh...