When I go now, I always carry travelers checks and credit cards. I convert the checks to yen at the airport, which has better rates than hotels (and better for the checks instead of cash). The majority of the time I just use my credit card, however. I use it for hotels, restaurants, and shopping. While it is a cash based society, restaurants don't seem to have any trouble taking my credit card. Heck, sometimes when I'm there with my coworkers we'll go out to dinner, have them split out the check at the cashier, and many will pay their share with credit card with no complaint from the cashier (same can't be said for the US).
The only thing I hate about cash is all those 100 and 500 yen pieces floating around in my pocket. Don't want to lose too many of those 500 yen guys.