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Security applies in two general contexts: application (software) security and content security.
Application security involves customizing security features to protect Acrobat and Reader against vulnerabilities, malicious attacks, and other risks. Advanced users can customize the application through the user interface. Enterprise administrators can also configure the registry. See the following articles for details.
Content security involves using product features to protect the integrity of PDF content. These features safeguard against the unwanted alteration of PDFs, keep sensitive information private, prevent the printing of PDFs, and so on. See the following articles for details.
A related subject is digital signatures, meant to guarantee the identity of senders and recipients of PDFs. See About digital signatures and ink signatures for a list of topics related to digital signatures.