Rhoads, A. F. & Klein, W. M. (1993): Vascular Flora of Pennsylvania: Annotated Checklist and Atlas (Memoirs of the American Philosophical Society). 636 p. [out of print]
Rhoads, A. F. & Block, T. A. (2000): The Plants of Pennsylvania: An Illustrated Manual. - 1061 p. University of Pennsylvania Press. [out of print, new edition in preparation]
Rhoads, A. F. & Block, T. A. (2004): Trees of Pennsylvania: A Complete Reference Guide. - 407 p. University of Pennsylvania Press.
The most recommended field guides:
Newcomb, L. (1989): Newcombs Wildflower Guide. 13th ed., 490 p.
Clemants, S. & Gracie, C. (2006): Wildflowers in the Field and Forest: A Field Guide to the Northeastern United States (Jeffrey Glassberg Field Guide Series). Oxford University Press, 480 p.
Petrides, G. A. (1998): A Field Guide to Eastern Trees. (Peterson Field Guides). 2nd ed., 441 p.
Websites:
Pennsylvania Flora Project website
Flora of North America website
PLANTS database for all of North America
Connecticut Wildflower Society (picture gallery)
Wildflowers of Western Pennsylvania