Usually in Tokyo when by myself I stay at a traditional inn. More fun (and cheaper).

But I was in Tokyo a couple of years ago with another and we found for a double it was a lot cheaper to book through Priceline or Expedia (lots of special 3-5 day deals available that only appear when you search for certain dates with a three or four or five day etc. stay).

Apparently P and E booked rooms often have a much lower charge for two people that directly booked rooms.