Okay, I think this has gone on long enough. You're all on the right path, but I don't think you're going to get there.
The key word in the original question was "segment" rather than "flight". I am, indeed, referring to SFO Helicopter Airlines and they did fly the S-61 (S-58 before that). What I was looking for, though, is the couple hundred yards between gates 55 and 44 at SFO. Most, not all but most, of their flights served both gates, and the helicopter would just taxi from 55 to 44 (I don't recall that it ever went in the other direction).
I don't have the timetable here at the office, but I think the flights to PAO and SJC were exclusively gate 55, and some to OAK were one or the other but not both. Most flights, though, show an arrival at gate 55 followed by an arrival at gate 44, or a departure from gate 55 and then a departure from gate 44. A lot of these, of course, overlapped: flight XXX coming in and flight YYY going out, but the same times at the two gates.
I remember standing on the observation deck and watching them just taxi from the one to the other before taking off from the taxiway. I never had the opportunity to take a flight, since we lived on the Peninsula just a few miles south of the airport, but I always wanted to.
The timetable varied over the years, of course, but typical routes were:
SFO-PAO-SJC (the first northbound of the day didn't stop at PAO)
SFO-OAK
SFO-OAK-(JOK)-CCR (one flight a day made the stop downtown, and one westbound was nonstop CCR-SFO)
SFO-OAK-(JOK)-JEM-JMC-JSF-SFO (JEM was Emeryville; before that it was Berkeley but I don't know the code -- and again, few flights stopped in downtown Oakland. This routing worked in both directions. The downtown San Francisco heliport was at the Ferry Building, and the Marin County heliport was in Sausalito a few blocks north of the tourist shops. Nice, modern-looking building, but I was never there at the right time to actually see the helicopter coming or going.)