generally, i go to panda if i can't find any good airfare sales directly from the airlines. i usually do a quick run through: airline site, orbitz/travelocity/expedia, hotwire if i'm really desperate (i typically rely on hotwire for hotels and cars, though). almost 90% of the time panda comes through for me. they don't always have the rock-bottom prices that sometimes come up last minute, BUT for people who have to plan further in advance than a month, panda usually has good deals. note: i usually shop for trips to the mainland--i've never been to japan, though it looks like they might have some good packages to there too.
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