It's hard to imagine how many miles of train tracks used to exist within Boston city limits (let alone how few will be left once Harvard gets around to ripping out the Allston yard). Here we see the train yard in front of Commonwealth Pier in South Boston, sometime shortly after World War I. Today, the pier is better known as the World Trade Center and the tracks have mostly been replaced by highway ramps, parking lots and surface roads. Nearby is Fan Pier, named for the way the train tracks there fanned out toward the water.
The Back Bay used to have its own large train yard - since replaced by the Prudential Center and the Massachusetts Turnpike:
The Back Bay yard used to end at the Lenox Hotel and Boylston Street:
And take a look at the tracks leading to South Station, which once extended almost completely to Fort Point Channel (yes, that's South Station in the photo, back in the days when it had a giant "shed" atop the tracks):
Here's what it was like inside the shed: