The line you see beneath the Turpike bridge at the Delaware is Amtrak's Northeast Corridor (Grundy Interlocking in Bristol, to be exact). The R3 West Trenton line runs parallel but several miles farther "inland". If you continue west on the turnpike, past the first rest area and the interchange for Rt. 1, you cross a bridge over a four-lane road (Street Rd) and then over CSX's Trenton Line (former Reading New York Short Line). About a quarter mile after that is where the turnpike crosses over the R3. It's easier to spot from the eastbound lanes than from the westbound side. The R3 and the New York Short Line meet up not too far from that spot and run alongside each other as far as Woodbourne, where SEPTA's ownership ends. From there to West Trenton, the line is owned by CSX.
The Trenton Cutoff is an ex-PRR, now NS line that runs from Morrisville to Downingtown. The eastern end is still pretty busy with merchandise, steel, and intermodal traffic. The yard in Morrisville is now also used by New Jersey Transit for its Northeast Corridor line trainset storage. West of Norristown, the Trenton Cutoff only sees one train a day, which I believe is a steel train. Near Norristown, Conrail used part of an old PRR ramp and wye that used to connect the Cutoff to PRR's Schuylkill Valley line, and connected it to the ex-Reading line at Ford St. So NS trains going west from Morrisville come off the Cutoff, duck underneath it, and head west over SEPTA's R6 as far as the Norristown Transportation Center (DeKalb St. station), then cross the river and join the NS line to Reading and Allentown or Harrisburg at CP Norris, near Abrams yard.
The Stoney Creek Branch is an ex-Reading branchline that begins in Norristown. There's a wye near the Norristown TC; the west leg crosses the river (see above) and the east or north leg is the beginning of the branch and the end of the R6. SEPTA's electric service ends at Elm St, but the branch runs northeast for 10 miles to Lansdale, where it ties into the R5 and the CSX yard north of the station. CSX has a pretty good-sized customer base in and north of Lansdale along the ex-Reading Bethlehem Branch as far as Telford, and from there north, it's the East Penn Railways' property to the end of serviceable track north of Quakertown. The Stoney Creek Branch was out of service for many years, but not abandoned because it was considered an alternate route for "back door" access to Bethlehem Steel during the Cold War. A shipper's group got together in the early 90's to re-open it for freight traffic, and its main purpose now is for any "high-and-wide" movements that need to go in and out of Lansdale. It's only good for 10mph, so most other freight traffic moves over SEPTA's R5 via Jenkintown, late at night. When SEPTA's bridge in Fort Washington was washed out in Tropical Storm Allison a few years ago, SEPTA used the Stoney Creek line when the Silverliners that were still running between Doylestown and Fort Washington needed service. There's no catenary, of course, so they had to be towed by a diesel at 10mph to Norristown, but at least they had that option rather than having the trains trapped above Ft. Washington until the bridge was rebuilt.
