Last sunday, I went Shinjyuku, Tokyo,
to survey how many indexcards are sold in stationery store there. I
went to the Sekaido (世界堂), one
of the largest stationery store in Shinjyuku. And it is close from
a subway line that I use to go office.
It is 5 to 6 floor building, all with
stationery and art goods. The indexcards are settled at the first
floor in Sekaido. I could find name card size, 5x3 size, 6x4 size,
B6 size with plain, printable, section (quadrille), 6 mm ruled, and
8 mm ruled. Also, Dock, index (separator), and purse are available.
I still couldn't find such a plenty of indexcard goods ever in
Tokyo. In fact, I only found B6 and 5x3 card, two kinds each in
another larger stationery store "Loft" @ Shinjyuku Mitsukoshi. The
Sekaido is rare case.
When you come to Tokyo, you should come to Sekaido. This is a
"Macca" for indexcard geek 
ref. : Website, Sekaido (in
Japanese)
ref. : High resolution map @ Yahoo! Japan, Sekaido