Yahoo Auctions - Not a shop, per se, but large source of bikes.

NAPS has locations around Japan. Carries a wide range of products from riding gear and accessories to bike parts. Also has a Service area for maintenance.

Ricoland has locations around the Tokyo Metro. Carries a wide range of products from riding gear and accessories to bike parts. Also has a Service area for maintenance.

Nirinkan - Driver Stand - Nirinkan has locations around Japan. Carries a wide range of products from riding gear and accessories to bike parts. Also has service area and some have bike sales.

Nankai has carries a wide range of products. Locations all over Japan.

Kushitani is a manufacturer of riding apparel and other accessories. Various locations in Japan.

Bosco carries Madif products, which includes Arlen Ness and Berik. They have a few locations around Japan.

Up Garage - Carries used bike gear and parts.

Kushitani does custom leathers. Custom suits in the 200,000JPY+ range.

Secretaire is a custom leathers shop in Meguro-ku, Tokyo.

Speedstar - Setagaya-dori in Setagaya-ku, Tokyo

Tire Shop Wolf Moto - Sakuragawa, Itabashi-ku, Tokyo

Mach - Near Edogawabashi-eki, Bunkyo-ku, Tokyo

Racing Max Fuchu - Fuchu, Tokyo

Astro Products - Not a specialty store per se, but has many items that are like name brand products but made in cheaper places. Has many tools and other accessories. Bike stands, etc. Many locations around Japan.

Tool Company Straight - Many tools and various equipment available inexpensively. Several locations around Japan. Shipping available.

GPS Store - GPS products, including RAM mounts, in Tokyo.

New Enough US online retailer of just about everything. Delivers to Japan.

Fuma - Setagaya (風魔) - Tokyo - Setagaya-ku. Google Map

Dirt Freak - Seto (Aichi-ken). Google Map

Rental 819 - Several shops in the Tokyo Metro area. Some seem 'related' in that you can get a bike from another shops' site to a local one. Doesn't work for all of them though.

Japan Bike Rentals - Rental in Akasaka - Tokyo, also rents luggage and GPS units, and provides suggested touring routes