Touhou gets the greatest amount of hits in these top media sites:
-Nico Nico Douga (129,689 vids tagged the general Touhou tag + 2684 tags that have "東方" in them)
-Pixiv (733,137 pictures tagged touhou ...as a reference, "Original" tag has 590,171, VOVALOID tag has 454,365 (Including the various capitals short forms...etc.)
...and has roughly 664,900 vids tagged touhou or 東方 on Youtube
(Data as of 10/06/26 a.k.a. when this thread was made.)
This is tags on videos and pictures so this is still very unreliable data, so we also put in information of cons and events.
Major Cons:
-Reitaisai 2010 had more than 30,000 people attending. (Numbers not including circles)
-紅楼夢 had roughly 10,000 people attending ('')
Minor Cons:
大⑨州東方祭り:4000 people ('')
...etc.
Also as far as I know -including the three mentioned- there are 35 "Touhou Only" events going on all over japan this year (Some already ended)
I don't know if these data will give you evident enough numbers, but when you compare these numbers to the audience measurements of some recent animes, I think you'll get a good idea on how many active touhou fans there are in Japan.
(Measuring the fanbase for lurkers and people who keep quiet about it is more difficult
Also since people can obtain games, books, and music through various means of file sharing *koff*and pirating *koff*
direct sales are making it harder and harder to measure fans from actual sales.)