Panda's Japan specialists can get you some good little mini unguided Japan tours for a good price that includes air, hotel and transfers (though not for all Japanese destinations). The first time I tried them, I was very impressed not by the price, but the length to which the agent would help me in securing tickets to a sumo event. Albeit, I decided to skip the sumo, she had called up someone in Japan and had a price for me and assured me that I would get the tickets at my hotel. If you go on solo trips, you might get a better deal getting hotel and air separately because of a single-supplement but it's still a good package. Oh yeah, and their website has some really good domestic airfare deals as well.
more