This is definitely my favorite fangame, but I haven't played many others outside of stuff mentioned in this post. It's easily on par with the best Pokémon games, but I don't think it surpasses them.
Haven't played it since the first demo, but I think this one is good too. Fun microgames, but some of the artstyles are kind of offputting and ugly.
I remember Concealed the Conclusion getting bad rap around here, but I liked it enough. The story is interesting despite being tonally foreign to official Touhou content, and I like the mechanics and patterns. Music is also pretty great; I especially like the stage 4 and 6 bosses.
Disagree on Touhou Mother, it's a cheap bastardization of both series that fails to capture what makes either great. The first one is probably the worst video game I have ever played and beaten, but the fact I finished it must mean something.
I should finish that sometime. Here you go.
As for others I've played, a rather well known one is MegaMari by the same guys who make the fighting games. Mechanically, it's a good recreation of the Mega Man games, but I never could get around to playing much of it. Not too big a fan of the level design, but you might find something in it I don't.
There is also a Pikmin clone I remember playing a while back, something along the lines of Shanghai and the Doll of Mystery. It's... alright, I guess? Very rough around the edges and not nearly as good as any of the originals, but I guess it sates my desire for a new one.