A few out of the box options, perhaps I missed it but you didn't state how long you'll be in Japan:

Will you primarily be on the go? Stationary? If you'll be near WiFi you can use the most convenient unified option for you would be to buy a Nokia E61i with WiFi and sign up for Truphone. It's the easiest no-hassle way to do VoIP I've seen and I used it very successfully this last trip to Tokyo when my Asterisk VoIP box fell over mid-trip. That also gives you a phone that works just about anywhere a phone CAN work as it supports UMTS and quadband GSM. When able to stay in one place long enough it worked very well for incoming calls as well as outgoing. If you don't travel internationally frequently it's a bit of a waste. If you do, it'll save you astonishing amounts.

The rentals I've seen are ¥60-¥80yen/minute so you're looking at between .55-.70 cents a minute in airtime and LD to call the US. Much cheaper than roaming but still not cheap. This last trip what worked well was to roam with my US SIM, limit calls on it as much as possible, and put off everything I could until I could be stationary for long enough to use VoIP. It wasn't perfect but a 10 day trip with heavy voice and data usage was only $650 in roaming. My last trip? Over $3k. I consider that a win.