Current Mercury-News location per Google Maps is in downtown SJ with no indication of rail access ever being at the site. That doesn't mean the printing plant couldn't have been someplace closer to the tracks, but Google doesn't find that now. Of course, the M-N is now part of a conglomerate that prints someplace else and trucks it all in, to the limited extent that they even print (mainly web).

Interesting looking at the Bees in Google. Sacramento and Fresno Bees both still have spurs connected even if they aren't used. Modesto Bee is in a modern plant in downtown, well away from any tracks, with no evidence of any formerlly rail-related docks -- all truck -- but it also looks newer than the Sac and Fresno plants.

The Comical plant on Mission in SF almost certainly had rail service in the deep past, though I can't tell from current photos how it got there. Most likely a spur up 5th Street from Townsend, but you would need somebody with old track charts to know for sure.

The current SF Examiner (http://www.sfexaminer.com) is a fundamentally different critter from the old Hearst rag. They use the old masthead but it's not the same. They're located in a high-rise like any other web site.