University of California
Ucmp: Aves: Fossil Record
A very good article on the fossil evidence and the prominent theory on the evolution of birds. Addresses both sides and presents information. Predominently agrees with the pro-dinosaurian point of view.
University of Guelph
Canada's Aquatic Environment/evolution of Birds
A good site that goes over the similarities and differences of reptiles and birds. Good look at the issue from a seemingly neutral view.
University of California
Ucmp: Systematics
A good overview of the radiation within the class through geologic time.
Talk Origins Archive
Talk Origins: All About Archaeopteryx
Good site which appears to take an unbiased approach to examining the wealth of evidence about the origins of birds. Provides tons of information about specimens, features, feather development, and more.
PBS
Pbs/evolution: Birds Arrived Comparitively Late
Good discussion of both sides of the debate over the origins of birds. Presents the recent evidence that seems to lean in the direction of the pro-dinosaur ancestry argument.
Other
University of Bristol: The Evolution of Birds
A short but effective synopsis providing much of the information collected over the years in terms of deciding the evolutionary ancestry issue. Article takes the pro-dinosaurian stance in the end, but includes good, if not brief,...
Other
Ornithology: The Evolution of Birds
Site provides a good overview of avian evolution debate without taking a firm stance on the dino-ancestry issue. Gives the broad ideas concerning bird origin and evolution.