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.
Mystical Power Plant, a danmaku fangame revolving around a giant tree inspired by Sugawara no Michizane. Also the sequel to The Last Comer.
Riverbed Soul Saver a danmaku fangame where a mysterious cold front has come to Gensokyo. The sequel to Mystical Power Plant.
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.
Touhou Puppet Dance Performance. It's in the same vein as Touhou Ningyougeki below however it's a standalone with interesting story, an interesting representation of Gensoyko, almost ALL characters introduced thus far and many well-known mechanics from the Pokémon games that were updated and remodelled specifically for this game.
M.U.G.E.N, a modifiable fighting game has characters from many different games, including Touhou.