Kamen Rider wrote:I don't think the Green line counts as it's not heavy rail.
Many systems have in-street running and in-median running like SFO & BOS, but I think the OP is looking for private-right-of-way that has crossings like Chicago's. For whatever reason, Boston's D line has one grade crossing that is a walking path in the middle of the woods. I ride that about twice a month. In 50+ years, I've never seen anyone near that crossing, but the trains slow down to 5MPH every time. Also, the Mattapan line has a few street crossings.
One of my favorites is (was?) the commuter rail line running down the middle of the street in Michigan City, Indiana, but that's still part of Chicago. I haven't been there for 15 years, I assume it still runs. But if we start counting electric commuter lines (like MetroNorth or LIRR), we'd fill pages.
I've always wondered how they keep kids from wandering down the tracks who don't know that the 3rd rail is alive.