Other than >>35148 I also consider these her themes:
Ultimate Truth, PCB stage 6 theme
https://www.youtube.com/watch?v=svbNyNi79Dk
>Why?
It's also Yuyuko's stage theme, but in my eyes stage themes first and foremost belong to the midboss.
Legend of Aokigahara (CtC arrange)
https://www.youtube.com/watch?v=GQikAHhTTKw
>Why?
It's Youmu's theme in Concealed the Conclusion, a fangame. ZUN's original of Legend of Aokigahara (https://www.youtube.com/watch?v=K9lwLau-mbQ) isn't featured in any game but only in one of his Touhou-themed music albums. However, ZUN's music albums have stories and this particular track describes how Merry and Renko visit the forests around Mt. Fuji ("Sea of Trees"(Jukai) or "Aokigahara"). They note that it is said that Aokigahara is linked to the Netherworld and even notice a gap in the border. Yukari-sama, what are you doing?
Their version of Legend of Aokigahara doesn't sound much like an actual Netherworld theme, because they perceive the Netherworld from the other side and it ends up as a mixture between elements of the Netherworld and the Human world. The arranged theme, however, sounds more like Netherworld themes like Ancient Temple and Ultimate Truth. It's almost like a reconstruction of the actual theme.
As a Netherworld theme it represents all inhabitants of the Netherworld and one is more likely to encounter Youmu outside Hakugyokurou. So, even if you disregard the fangame background, it still makes sense.