Whoooof...narrowing it down to 10 is tough.
10)
Voyage 1969. Final Stage themes usually speak of a journey drawing to its epic conclusion, and the final moments coming fast upon you. Voyage 1969 does this, but it does so much more. It feels like as you reach the end, the world, the endless sea of stars opens for you as well.
9)
Fires of Houkai. For pure instrumentation, and for bringing the aforementioned sense of culmination out better than any of the amazing final stage themes ZUN has composed to date.
8 )
Himorogi, Burn in Violet. The almost unknown Stage 4 theme from Story of Eastern Wonderland. As poor a game as it was, with mostly sub-par music as well, it nonetheless contains this theme, an absolute gem. I first had though the stage title was the song title: "Revengeful Ghost". That of course refers to Mima, but this theme speaks so much of revenge for a long-nurtured hate, and it is truly the best theme in the game and number 8 on my list.
7)
Gensokyo, Past and Present ~ Flower Land. Yuka's PoFV theme. Probably my favorite aspect of PoFV is simply the percussion; ZUN goes out of his way more than any other game to do fun stuff with it. Almost every song has offbeat stuff, random sections, and other things I'd be able to put names to if I had any education in drumming. That said, Flower Land is another masterpiece of percussion usage, and it is an amazing theme to boot. Yuka is an added plus.
6)
Maple Wise. The oft-overlooked (and almost completely unremixed

) stage 4 theme of Mystic Square. Like its counterpart, Forbidden Magic, the theme speaks of sadness more than anything else, but it is so...moving; it's high and low, ice and fire, sadness and joy.
5)
Maiden's Capriccio ~ Dream Battle. The main character of the Touhou Project is here...and she's pissed. This is such an amazing track notably for being an arrange of the original Maiden's Capriccio, and unlike LCMS ZUN did an absolute wonder with this. Everything about this track stands out to me, especially the piano and percussion.
4)
Demystify Feast. For all the power released in this song, nearly the entirety of it is nothing but an intro, both to the final, EPIC piano, and to the feast as a whole. It fits IaMP perfectly, it fits Touhou perfectly, and it fits into any top 10 list with ease.
3)
Lullaby of Demonic Hell. From the very opening, with the lonely howl of the wind, you know that this piece is destined for greatness. It is exactly what is says: a lullaby, though in the darkest and most demon-ridden of places, and it is superb musical arrangement. It also wins points for ranging so far afield of ZUN's work, but SA as a whole is a mess of genre-breaking win.
2)
Reach for the Moon, Immortal Smoke. Still, in my opinion, ZUN's absolute greatest piece of music. It conveys so much emotion, so much depth; it really brings to life the concept of Mokou, immortality, the Phoenix, and everything else about IN's Extra, and is absolutely beautiful.
1)
Lunar Clock ~ Luna Dial. This has always been my favorite of all the Touhou songs, period. For many reasons. The fact that the whole track sounds like a clock is a big plus...but honestly, I have trouble pinning down exactly what it is that makes it so awesome. Suffice to say, nothing can upset this.
There are a crapload of honorable mentions; these are just the ones that I had to kick off the list at the very end:
Infinite Being
Centennial Festival
Phantom Ensemble
Ultimate Truth
Suwa Foughten Field
Hartmann's Youkai Girl