The City of Philadelphia Department of Records has begun digitizing their photo collection and placing it online. So far only a small fraction of their collection is available. A search on the keyword railroad has 233 entries. The archive is at:

http://www.phillyhistory.org/PhotoArchive/Home.aspx

The photo's are mostly but not exclusively in Philadelphia. For example there is a picture of the "P.R.R. Shops, Altoona, PA" from 1885.

http://www.phillyhistory.org/PhotoArchive/Detail.aspx?assetId=4555

I found this aerial photo of the construction of 30th St Station interesting.

http://www.phillyhistory.org/PhotoArchive/Detail.aspx?assetId=14845

The archive says this was taken July 10, 1934. Can this be correct given that construction was finished in 1934 and the photo does not show any of the the main building?

Note that most of the photos come with a map beside the thumbnails, showing where the pictures were taken. This is a new and amazing feature that I haven't seen before. Thanks for the link.