There are plenty of Japanese-made bikes still in production. All the keirin workshops, and a few touring/randonneur-specific shops (Zephyr, Pegasus), and others that are not NJS/keirin but still make all sorts of great bikes (Zunow, etc).

The major ones are Panasonic and Bridgestone/Anchor. Lots of models, lots of materials, relatively cheap pricing, tons of custom paint options (glow in the dark B-stones!)......and not for sale in the US!

Good excuse for a trip to Japan!

Panasonic: http://www.panabyc.co.jp/products/sports/index.html
the Panasonic Order System bikes are custom order, but the 2008 model year site isn't up yet: http://www.panabyc.co.jp/products/pos/index.html

Bridgestone's high end models go by the Anchor brand-name:
http://www.anchor-bikes.com/bikes/bike.html