There are many subway and commuter rail lines that cross from one borough to another, but some crossings are particularly underserved. One that's often mentioned is between Brooklyn and Queens.
There are in fact five subway lines that connect Brooklyn and Queens directly: the A/C Fulton Street Subway/Liberty Avenue El, the G Crosstown Subway, the M Myrtle/Ridgewood El, and the J/Z Fulton Street/Jamaica Avenue El. The LIRR Atlantic Branch also goes from Downtown Brooklyn to Jamaica. Connections from Jamaica and Ozone Park to Downtown Brooklyn are good, and connections from Greenpoint and the other G train neighborhoods to Long Island City are good. Connections from northern and western Queens to southern Brooklyn are not so good.
What we don't have right now is any concrete information about what neighborhood pairs people want to travel between in Brooklyn and Queens, so we don't know exactly where the greatest need is, or the greatest potential ridership. So we don't know which corridor to work with.
There is some information available, the census journey-to-work data. Working for the Regional Plan Association, Michael Frumin used this data to model potential ridership for one particular line: the Triboro RX proposal to run subway-frequency service along the NY Central Port Morris Branch, Hell Gate Bridge, NY Connecting Railroad and LIRR Bay Ridge Branch, from Yankee Stadium all the way to the Brooklyn Army Terminal. Frumin wrote, "At the end of the day, we can comfortably say that at least 76,000 New Yorkers (including 32,000 diverting from other modes of transportation) would use the Triboro RX to get to and from their jobs every day." Obviously, there are not that many people who live in Bay Ridge and work in Concourse Village or vice versa; most of the trips that Frumin projected would be less than a third of that length.
It'd be nice to have some easy interface to the journey-to-work data to be able to tell, for example, where the best place to build a new Brooklyn-to-Queens connection would be. It would also be helpful for estimating the effect of only building part of the "Triboro RX" at a time.
In fact, just because there's an unbroken set of tracks running from St. Mary's Park to Owl Head Park doesn't mean that you need to run a single train line the whole way. It might be better to use the line for extensions or branches to several different lines instead.
I'll give one example, which was actually considered by the MTA back in the 1960s: to extend the L train west to Brooklyn College. This and other uses of the Bay Ridge Branch were considered in a long and multi-branching SubChat thread last year. Someone was kind enough to post scans of a map that was released by the MTA and the city in 1969, and another that was printed in the New York Times in 1971. (The rest of the scans are worth a look as well). More potential uses later.