I am interested in this thread, because I have been trying to get into Touhou since I started reading this stuff back in October, and I have yet to really get a good grasp on it. I can never keep the characters straight and have no idea why I should care. And it seems like every time I read a new TP doujin, they introduce some new character or pairing I've never heard of.
I guess...Reimu x Yukari is one of the main ships? And Keine x Mokou? And the vampire chick and her maid? (Remila x Alice, I think?) After that it gets REALLY fuzzy for me.
I did like that "End of the Universe" comic, but that wasn't really romantic as much as it was someone showing off their astrophysics classes in comic form.