In compiling my thoughts from the last post into a map, I realized that a couple of possibilities I hadn't included should be, mostly for the sake of completeness. These are two (relatively) minor spurs, one in the city and the other waaaaay at the edge of the boonies, and consideration of where Mercer Co. fits into all this.
1. The Colebrookdale Spur is the line waaaaaaaay out at the edge of the boonies, running from Pottstown to Bally. North of Boyertown its rails have been ripped up. I hadn't included it in the original compilation because it is just too far to be viable for the Philadelphia commuter market (although it may be more so for Reading). Nevertheless, the Gilbertsville-Boyertown area is sizable--in European markets, it would be large enough to demand at least daily rail service.
2. The Greenwich Extension is the ex-PRR route that extends from the Northeast Corridor through South Philadelphia to Greenwich Yard. Heavily used by freight and constrained by the single-track Arsenal Bridge across the Schuylkill, it is a poor fit for commuter rail. Nevertheless, it is for most of its length carried over 25th St. on a massive viaduct, a structure built for far more capacity than it today handles. I have in the past suggested a heavy rail line to take advantage of this excess capacity.
3. Mercer Co., N.J., is...complicated. There is a major job market in and around Princeton, the dominant local commute pattern; the remainder is about evenly divided between the Philadelphia and North Jersey/New York commute markets. (In fact, the New York and Philadelphia urban areas are divided by an extremely narrow impromptu greenbelt running about halfway through the county.) Because of this, organizational competence is absolutely essential for providing good mass transit. This would instantiate with two things: rational transfers and a local fare union between SEPTA and NJ Transit, potentially between Cornwells Heights on the Trenton Line and Trevose on the West Trenton Line, and to Princeton, New Brunswick, and Bound Brook on the NJT side. A new spur of the Raritan Line from Bound Brook to West Trenton would also be essential. Operations can be done via co-routing of SEPTA and NJT trains (terminating SEPTA trains at New Brunswick, for example, or NJT trains at Cornwells Heights); in either case, however, cross-platform, or at worst, timed transfers absolutely must be implemented. (The timed transfers between the Trenton Line and the Northeast Corridor Line are one of the few artifacts of organizational competence to be found anywhere in U.S. railroading; too bad it is neither furthered nor backed up.)
4. Speaking of intercity transit, down in Maryland, MARC's terminus in Perryville is essentially nowhere: too far to be useful for the Baltimore commute market, but too close to be useful as an intercity to Wilmington. Extend it to a natural terminus in Wilmington.