On Friday, I was on my way to Tsukuba when I spotted a banner advertising rental bikes available. I was curious, so when I went around, I saw that it was an entrance to an underground bike parking garage.
The stairs have ramps so that it is easy to walk bikes up and down.
There is even a motorized track for the way back up.
This is a view of the garage itself. I was in a hurry, so I didn’t get an accurate count, but I would guess that the facility holds about 1000 bikes.
Judging from the relatively recent vintage of the facility and its location, I would guess that it was part of a station renovation to accommodate a platform (Shin-Okachimachi) for the Tsukuba Express, which went into service in 2005. It is a clever way of accommodating a large number of bikes at a station where there would otherwise be very little parking available.
One small addendum to the previous post. Here is another “Papachari” I saw on my last day in Tokyo. Unfortunately, it went by before I could get a decent picture, but if you look closely, there are two front wheels in a leaning tadpole trike configuration. You can also see that the manufacturer has taken the trouble to mount front and back and front fenders. 
Update: there is a little more information about this bike here.
Thanks for this great item jnyyz. Can we hope that North America might one day evolve to this?