Hi,
according my short experience (2 trips to Japan), I have found the best prices through kakaku.com (and Google translator!). You can do a search for a model in Latin alphabet (like 'FX-33') and translate the results pages.

Japan cheapest stores are (roughly) around Akihabara district and only accept payments in cash. Last October (2007), I found (and bought) with kakaku cameras 10-15% cheaper than Bic Camera or Yodobashi (20,000 yen vs 25,000 at Bic). Prices vary every few weeks and you can see a little graph within website results page showing the product price evolution. Shop assistants may do not speak English, so I recommend you to bring the kakaku results page printed.

For a 'fixed' price product, like the Apple ones (iPod), Apple stores in Japan are very useful. Shop assistants spike English, and they offer you a CD with software, manuals and tutorials in English and other languages (Spanish...)

The only concern would be, in the case of video or photo cameras, that they have on-screen menus other than in Japanese (Sony newest models don't).