The Wildlife Resources Management Manual, prepared by Chester Martin and others for the Environmental Impact Research Program, contains several chapters that provide guidelines for surveying and sampling animals:
6.3.2 Avian Line-Transect Methods
6.3.3 Avian Plot Methods 
6.3.4 Avian Territory Mapping 
6.3.5 Auditory Survey Methods 
6.4.2 White-tailed Deer Track Count Census 
6.4.3 Deer Spotlight Census 
"Bioassseesment and Biocriteria" is the topic of a set of helpful Web sites maintained by the Environmental Protection Agency (EPA) Office of Water: http://www.epa.gov/ost/biocriteria. We recommend starting by clicking on "EPA's Bioassessment and Biocriteria Program," then the link for "Technical Assistance and Guidance Documents," then "Guidance Documents". Searches from this page http://www.epa.gov/ceisweb1/ceishome/atlas/bioindicators/publications.html will yield documents on all faunal groups, with emphasis on invertebrates and fish in aquatic systems.
The American Fisheries Society home page has links to references on inventory and many other materials via a jump to Marketplace, Publications, or Aquatic Stewardship:
The Breeding Bird Survey is now on-line at http://hinesj.er.usgs.gov/bbs/bbs.html. Data for North America for the years 1966-1999 are available along with a number of trend analyses. Data from specific survey routes can be accessed by clicking on the state and particular route in or nearest to your area of interest. Trends in selected guilds and overall species can be displayed; for example, wetland birds in Nebraska and Neotropical birds in Massachusetts.
Additional sources of information are found in the "Literature Cited" section.