Wow, it's been ages since I've posted anything, and during that time, my favourite has changed over time.
I remember the old post I, well, posted, with it being Flandre/Remilia, then Sakuya.
But now, Yukari is at the top, followed by Yuyuko, Byakuren and lastly Sakuya.
I'm not sure if I have a good reason, but Yukari had just seemed to climb her way to the top. I believe it's because she's blonde and oh-so immensely powerful. Maybe I'm attracted to powerful things... I also like how she is portrayed by the fans as a somewhat mature lady, she's beautiful, sexy, and has a mature feeling about her.
Yuyuko, I'm not too sure, she was pretty much tied in the same place as Yukari was at first, but she took second place. I like her danmaku battles, the patterns, her theme, having her as a last boss fight is amazing.
For Byakuren, I loved they way fans portrayed her as a hot gothic loli girl. Or something. That, and I felt proud of myself to get to her stage on easy... Using a lot of continues to reach her... Probably the hardest Touhou boss I've fought. Oh wait, there's always Yukari in Phantasm Stage...
Can't forget Sakuya, though. I still find her awesome.