PBS
Pbs: Nova: The Four Winged Dinosaur
In 2002, paleontologists discovered a fossil in China that seemed to provide a missing link between dinosaurs and birds, and to support the theory that birds evolved from dinosaurs. The fossil came from a four-winged dinosaur they named...
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
Natural History Museum of Los Angeles County: Dinosaur Institute: Dinosaurs
The origins, evolution and diversification of dinosaurs through geologic time are described, as well as their portrayal in Hollywood movies. There is also information about how birds evolved from dinosaurs.
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.
Other
Buzzle.com: Bird Eden: What Is an Archaeopteryx?
Explains what the Archaeopteryx was, its habitat and diet, the features it shared with dinosaurs and birds, and what is known about its locomotive abilities.