Touhou Omen Trilogy, an RPG series which includes Genius of Sappheiros, Devil of Decline, and Nightmare of Rebellion.
The Last Comer, a danmaku fangame that explores a Book of Revelations type incident in Gensokyo.
Touhou Labyrinth, a Touhou dungeon-crawling RPG game similar to Wizardry; it has an expansion and later an updated re-release* (the updated re-release contains both the base game and expansion pack in one along with several new features).
Satori Komeiji's Mental Education, a puzzle game with Satori and Koishi Komeiji, Utsuho Reiuji, and Rin Kaenbyou.
I.⑨ -Intelligent Fool-, a crossover with Intelligent Qube staring Cirno. This game was built with the Unity engine and has a Macintosh version included with the Windows verison, making it one of the few games officially available on Macintosh.
The Legend of the Dusk: The Legend of Twilight, a The Legend of Zelda: A Link to the Past fangame staring Rumia.
Touhou Maihana Ao Makyou ~Uniting Barrage Action~, a horizontal shooter fangame, featuring characters mostly from The Embodiment of Scarlet Devil and Mountain of Faith.