Ross ---
The character of a Pennsylvania shortline depended entirely on geography. Of course, I guess that's true of every RR everywhere. Pennsylvania, historically, was shortline heaven, and the commodities handled were mind-bogglingly diverse.
Right smack in the middle of the State was Centre County (hence the name), which was home to the Bellefonte Central RR (BFC). There were no coal mines on the line, but coal was mined on the PRR's nearby Snowshoe branch, and the railroad brought coal and other commodities to Penn State University at the town of State College. The BFC's most important commodity was limestone and related products, but there were feed mills, retail lumber yards, etc. on the line.
Bituminous (soft) coal predominated in the western part of Pennsylvania; Anthracite (hard) coal predominated in the Northeast. Other types could be found in pockets here & there, such as the semi-bituminous coal of the Broad Top Mountain area (south central). The steel industry was a major economic force throughout the State, as was (and is) agriculture. In the deep forests of the north central part of the State, trees were cut for the tannin in their bark, and a very important leather tanning industry developed. The Wellsville Addison & Galeton RR called itself "the Sole Leather Route". I believe the Chestnut Ridge Railway served lead/zinc smelters or some such thing.
My best advice is to READ READ READ. Think about the industries that are most interesting to you, and unless you choose citrus farming, I'll bet you can find a Pennsylvania shortline that served those industries. I don't know where you live or how much trouble you might find in seeking out material on obscure Pennsylvania shortlines. Some books that could be helpful are:
PENNSYLVANIA SHORT LINES IN COLOR Vol. II and Vol. II, by Gary R. Carlson, Morning Sun Books, Inc., 9 Pheasant Lane, Scotch Plains, NJ, 07076 2003; 2005.
RAILS to PENN STATE, The Story of the Bellefonte Central by Michael Bezilla and Jack Rudnicki, Stackpole Books, 5067 Ritter Road, Mechanicsburg, PA, 17055, published 2007, 310 pages.
Anything by Paul Pietrak (Buffalo & Susquehanna, Buffalo Rochester & Pittsburgh, and other area RR's). These are probably all out of print
The MA & PA, A History of the Maryland & Pennsylvania Railroad, by George W. Hilton, 1963. My copy was published by Howell-North, but I believe a more recent edition is or was available.
You'll probably have to look for used books to find these.
Tom