Also the PATCO speedline/NJT ACL, Beesley's Secondary, Mt. Holly/Hainesport Industrial, the C&A in Cranbury though I think the tracks stop just short, some tracks that serve an industrial park in Jamesburg, the MIlltown Branch (former Raritan River RR), maybe more North but that's where my geographic familiarity ends. None gets much usage except the NJT/PATCO, which sees dozens of passenger trains daily.
Of the ones rrbluesman said, the Millville branch is the busiest, hauling mostly sand sand hoppers from a quarry operation near Newport, NJ, a few miles from the bay, via an interchange with the Winchester & Western RR. There's other business along the line, served by a Conrail local out of Millville. The busy Pennsgrove Secondary technically never meets the turnpike, there's a short spur off of it called the Deepwater Industrial track that goes under the Delaware Memorial bridge, but the Deepwater Generating plant switched to natural gas and no longer takes coal deliveries, so I don't think it's been used in a few years.
The Salem branch, at that point owned by Salem County, crosses under the turnpike near Woodstown and is seldom used now that the glass factory in Salem is no more. A few cars may pass through here each week, mainly headed to Kopper's poles and Mannington Mills.