In reading Wikipedia's entry on railroad switches, I found the following quote rather inspirational:
"A gantlet track can also be used when two railroads of different gauges share right-of-way; the standard-gauge Delaware, Lackawanna and Western Railroad used the wide-gauge Erie Railroad's tunnel through the New Jersey Palisades in this way before the DL&W built its own tunnel."
Gee, so... in the SF Bay Area, BART has a tunnel. Which is nearly at capacity, not because of the physical limit on the space between trains, but because of the physical limit of the stations at each end only being able to hold one train at a time.... basically, headways through the tunnel are limited by the time it takes a train o slow down, stop, open doors, load/unload passengers, close doors, and move on. Two to three minutes or so, it how long I believe this takes.
One potential solution to this problem, which I believe Portland, OR is attempting to enact to solve the light rail capacity problems over the Steel Bridge, is to build a wye and two sets of stations on either side of the bridge/tunnel.
BART pretty much hosed this option for themselves using BART technology by locating their wye after West Oakland station, and not accommodating a wye prior to Embarcadero Station.
However... with Caltrain being planned to extend underground to within two blocks of the tube entrance in San Francisco, it would make potentil sense for Caltrain and BART to share the tube underneath the Bay, using a gauntlet track construction to accommodate the various gauges and kee the Caltrain cars away from the third rail. Caltrain could enter the tube just after Embarcadero, then exit where the tube crosses the grade prior to West Oakland (and from there be given the option of its own split, to either Jack London to the south or Emeryville to the north).
Operationally, it might be tricky to run Caltrain and BART through the same tube, EXCEPT that I believe BART trains may actually be slightly longer in length with 10 cars. There may be a height issue through the tube for the double-decker Caltrain rolling stock, but that might just be a matter of only running lower-height-profile rolling stock on transbay runs.
Anyways, it is definitely a point worth considering.