I'm living in Tokyo and bought a C5050/PT015 package a couple of weeks ago. Theoretically cheapest place here is Akihabara district but my recomendation is to go straight to Yodobashi Camera in Shinjuku. Currently they list C5050 Y89,800 and PT015 Y19,800. That's approx US769 and US169. I pay 5% tax, you get it tax free if you leave Japan inside 6 months.
Yodobashi has a Gold Point Card which currently gives you 15% discount on camera, 10% on housing - points are instantly redeemable for goods, so you can buy camera and get cheap housing or buy camera and housing and get free batteries, memory cards, whatever. Memory price examples CompactFlash Y8,000 (256mb), Y40,000 (1gb), 88,000 (2gb).
Store is huge, well laid out and as everywhere here, staff very helpful. Camera sales staff tend not to be too familar with products (too many of them) so have a clear idea of what you want before you shop.
By amazing coincidence, Yodobashi prices for camera and housing are exactly the same as popular Japanese mail order place
uwdigital, referred to by a few other people in this forum, they are at :-
http://www.uwdigitalcamera.com/English/euwdigitalindex.htm
Yodobashi site is :-
http://www.yodobashi.com
but Japanese only, cameras are the first link at the top, after that the pictures may help!