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There are many books and articles discussing institutional abuses against animals and the ethical principles this violates. Some good general sources are:

Peter Singer, Animal Liberation: A New Ethics for Our Treatment of Animals -- perhaps the most influential book of the animal advocacy movement; focuses primarily on ethics, vivisection (animal experimentation), and factory farming

Tom Regan, The Struggle for Animal Rights -- well-written, covers diverse ethical issues

Marjorie Spiegel, The Dreaded Comparison: Human and Animal Slavery

Jeffrey Moussaieff Masson and Susan McCarthy, When Elephants Weep: The Emotional Lives of Animals

Animals on Farms
Jim Mason and Peter Singer, Animal Factories

Billy Ray Boyd, For the Vegetarian in You

Keith Akers, A Vegetarian Sourcebook (Vegetarian Press, P.O. Box 61273, Denver, CO 80206)

Ron Baker, The American Hunting Myth

Vegan Outreach
Vegetarian Source, Inc.
Vegetarian Resource Center
Animal rights sites on the 'net
Satya, the magazine