If you are heading to Hakodate by train, be sure to enquire about the Seikan Tunnel Tour. It was quite a few years ago when I did this, so hopefully JR still offers it. There are a few trains each day that stop at one of the emergency platforms deep in the tunnel, letting off passengers who have signed up for the tour. As I recall it was about Y2,500 extra for this two hour experience.

The friendly JR staff who work in the tunnel take you into the service tunnel which runs parallel to the main tunnels to show you how they keep the place maintained & etc. There are a number of exhibits and photos of the tunnel construction, and I thought the best part was when they showed us the emergency exit tunnel. It has a cogwheel train which ascends at a sharp vertical angle up to the surface. Seeing the path of this train up, up, up was quite an eerie feeling, as you can get a feel for just how deep you are down in the bowels of the earth

Naturally, knowing Japanese is a plus, as there is no English guidance. Will you be traveling with anyone who can assist you there?