Secret Full Scale Underground Racing Tunnel
an ultra secret underground aerodynamics testing facility hidden under a mountain in an abandoned road tunnel, allegedly being used by a leading Nascar and IndyCar team.
A more infamous example are the numerous drug-tunnels running from Mexico to the U.S. But the main places to look for secret long distance transit are at the various governmental underground facilities in the world, a few of which I will list here:
Mount Weather Emergency Operations Center. The underground part of the facility was built as far back as 1959. Numerous countries have Continuity of Government facilities, many of which are underground. It is not a far stretch to assume that "continuity of Government" would also include transportation and transit between locations.
Cheyenne Mountain Operations Center
Raven Rock Mountain Complex
Many of the facility's activities are classified, and distribution of most unclassified information about the facility is discouraged by the government. On May 25, 2007, the Federal Register published a DoD policy declaring that it is unlawful for any person "entering in or on the property ... to make any photograph, sketch, picture, drawing, map or graphical representation of the Raven Rock Mountain Complex without first obtaining the necessary permission."
On the feasibility of underground transit systems:
Kremlin greenlights Siberia-Alaska Tunnel
Yes, that 65-mile tunnel under the Bering Strait separating Siberia and Alaska, first proposed in 2007, is back on again. And this time its chances of actually being built are strengthened by a 500-mile link from the existing Trans-Siberian line to the Eastern Siberian city of Yakutsk, scheduled for completion in 2013.
4000 mph underwater train from London to New York
A more detailed article on this is here: Transatlantic Maglev
But wait...there is already a secret tunnel going from New York to London. Its baffling how it could be built while hardly anyone noticed: Secret Tunnel from New York to London
The following article proves that a high-speed underground subway from L.A. to New York was already being planned in 1972:
LA to New York in Half an Hour
As you can see, the evidence, thus far, is anecdotal, awaiting more solid proof. I hope I have inspired you to add your own insights and maybe even research to this idea. For now, what we know is that secret subway stations, secret subway lines and secret underground facilities do exist. The question is to what extent they exist and I would like to think underground transit is a little more sophisticated than we are told. I would think that it would be an important part of "continuity of Government" and substantial "black budget" allocated to it.