An internet search on the subject twenty years ago would find you only about nine links on the topic deemed worthy of consideration.
There were only about a thousand results out there according to Alta Vista, but most were duplicates; much of the remainder were one or two bogus paragraphs long.
Nowadays, a search on Google will return over 103,000 results, many of them well-detailed on the topic. I think these ones are the best content we've found.
(Note: Some of these links may expire due to the sensitivity of the subject matter).
Skeptics Dictionary on Animal Mutilations:
Aggressively critical of those who either (1) believe in the existence of the phenomena or (2) think it's linked to UFOs.
Dead Cows I've Known:
Putting it all together - Mad Cow disease, Mutilations, the Secret Government and Black Helicopters. Read this only if you dare.
Operation Animal Mutilation Official Report:
The final report of the U.S. Justice Department's investigation of the phenomena in New Mexico in the late 1970's. Also known as the Rommel Report, it blames natural predators for the mutilations.
These are the real X Files on the FBI's very real Animal Mutilation Project. You will need to download an Adobe PDF viewer to read the files.
They chronicle the FBI at work, avoiding investigating mutilations, despite frequent reports, and only opening the investigation after being harassed by various US Senators and Congressmen. They include many newspaper clippings reporting mutilations across the country. The file Cattle2.PDF has a particularly detailed article from the September 1976 issue of Oui magazinewhich is well worth reading.
A report from the RCMP looks like most of the Freedom of Information Act reports on UFOs have been deleted during the Obama administration, so we are linking above to the internet archive and mirroring the 128 pages of documents here:
National Institute for the Discovery of Science Animal Mutilation Page:
The NIDS advocates a scientific approach to the investigation of Animal Mutilations. Detailed necroscopies and analyses of the phenomena can be found here, on a internet archive link, as the original site is no more.
Cattle Mutilation Photos:
See for yourself, site archived via the Way Back Machine.
Animal Mutilations Page:
Lots of links to articles on mutilation and chupacabras, site archived via the Way Back Machine.
The Straight Dope
What's the story with cattle mutilations?
Cattle Mutilations Called Episode Of Collective Delusion
The Rommel Report
Operation Mutilation: The Official Report by Jon Elliston
Rommel, Jr. Kenneth M. Project Director, "Operation Animal Mutilation: Report of the District Attorney, First Judicial District, State of New Mexico," published in June of 1980.