Except for exchanging a little cash at the airport, I simply use the ATMs and withdraw as much as I can each time to minimize transaction fees.

I have a daily limit of $500, so it was tough when the yen was at 79 to the dollar on my last trip in October 2012. It meant that withdrawing even ¥40,000 would put me over the limit, so I survived on ¥30,000 withdrawals, which meant having to withdraw more frequently. (I paid for hotels with a Capital One credit card--no foreign transaction fee--so the ¥30,000 was for meals, transportation, and other incidentals. I didn't get a JR Pass, because I never left the Tokyo area on that trip.)