Hm... Honestly, I'm not sure. Septette is beautiful, but it's severely harmed by the instruments from EoSD IMO. Border of Life and Cosmic Mind are also beautiful, and don't have Septette's problem. Surprisingly, I think Complete Darkness is in the running as well, despite having the PC-98 chiptune deal... Hm...
I'd say Cosmic Mind really. I can't put my finger on WHY it's so beautiful, but it is.
Also, this is kinda off-topic, but even though I normally prefer songs that are kind of intense and fast-paced (not sure how else to describe it) final boss themes in Touhou usually catch my attention just by being plain... I dunno, beautiful. Eh... Not that good at trying to say what I mean <_<;