Depends on your budget. The Oakwoods and Residence Inns are the high end, and on the low end are the "gaijin houses," where students and young English teachers rent rooms and share kitchens in sometimes squalid conditions.
In the middle are the Tokyu Stays, which charge about 9,000 yen for a single night, with the price going down the longer you stay. They include a full bath, a kitchenette with sink, refrigerator, cooktop, and microwave, a washer-dryer, and a broadband Internet connection. There's maid service once a week.
Some don't like the Tokyu Stays because they don't allow you to bring visitors to the room, but that's not a problem with me.