This is a complicated story, an important chronicle of which is published by two recommended sources for which I provide the direct links as follows: journalist Declan McCullagh and the weblog LawMeme (from Yale Law School).
The short version is that the Internet Archive has removed all its links to a personal site called Operation Clambake, that maintains a library of documents critical of Scientology. Purportedly, documents on this site include materials for which the the Church of Scientology claims copyright. Another site, Reed Slatkin Media Resources, stated in an email to Declan that links to their site have likewise been removed from the Internet Archive for the same reasons stated above.
The Digital Millenium Copyright Act (DMCA) provides checks and balances for the disposition of claims of infringement, which apparently were not exercised by the Internet Archive in the case of these two web site. This is a developing story, which will not doubt result in further postings.