quick & dirty comparison of MBTA commuter rail fare zones with JR East fares from Shinjukupic.twitter.com/54bAY8l3nz
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This isn't limited to trains, either--most bus routes also have a distance-based fare (you grab a ticket while boarding, then pay when you leave, based on what the on-board electronic fare chart says you owe). Some bus routes apply a flat fare, though.
Oh, one last note: JR Fares are a bit more expensive, mile for mile, than private railway (eg Odakyu, Tokyu, etc) fares. They are still cheaper, mile for mile, than subway fares.
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