The U.S. Geological Survey manages several monitoring programs with data useful for providing context for project sites, providing baseline data on similar resources, and assisting in projections at other locations. See the parent page for the Biological Resources Division, http://biology.usgs.gov/, then go to "Science" and "Publications." There are links to two major monitoring documents. One is "Our Living Resources: A Report to the Nation on the Distribution, Abundance, and Health of U.S. Plants, Animals, and Ecosystems." This is organized by taxonomic groups and ecosystem types and was completed in 1995. Begin with the Table of Contents in the pdf file; when a selected topic is clicked, the file expands into that section.
The second document is the 1998 "Status and Trends of the Nation's Biological Resources." Part 2 of that report presents status and trends by selected region of the U.S. and would be especially useful for people beginning work in a new area.
Another USGS page has several articles useful for planning monitoring activities: http://www.mp1-pwrc.usgs.gov/im.html. Information on ongoing programs is organized for amphibians, butterflies, birds, other species, software, designing a program, and other internet sites. Programs are given such as Frogwatch USA, the Butterfly Monitoring Project, Marshbird Monitoring,