I saw some decent used laptops in Shinjuku at Yodobashi Camera. They have a used equipment section on the top floor. Also went to another store there, maybe BIC Camera or Softmap that had some used equipment. I suspect the PCs were in house demos because they all looked to be in good shape.
If I were going to buy a used model I would try to get a store demo as opposed to one that has been abused by a 3rd party.
From what I remember the prices were reasonable. I had just bought a notebook about 3 weeks before and wish I had found the shop sooner.
As for brand recommendations from my experience: Toshiba or IBM. Don't get a Sony or Sharp.