First it must be emphasized that all the same basic rules apply to PDF as apply to any file -- open it only if you trust the source.
Beyond educating users, several concrete strategies are available to dramatically enhance your protection against malicious PDF files and vulnerable PDF viewing applications.
Get the update
The frequency of software updates has increased as the threats have multiplied. Any protective strategy should ensure that regular (and emergency) updates can and will be distributed to affected desktops as expeditiously as possible.
Organizations "of a certain size" decided long ago that ad-hoc unmanaged desktops was an IT nightmare that could be defeated with centrally-managed software deployment. In these settings, the simplest way to deal with threats is to turn off functionality in the affected software.
In some cases, for example, the recent authplay.dll vulnerability, can be mitigated by simply renaming an installed file -- a process that's ready and waiting to go in most managed-deployment installations. In other cases, customizing the software as-deployed is often necessary, and for that, Adobe Systems, at least, provides an extremely granular deployment customizer.
In other cases, PDF certification or digital signatures can provide another option for ensuring active content PDFs are known to be safe.
The most troubling aspect of these new threats is that they arrive on a vector that most users and managers have grown to trust -- PDF.
This trust is entirely out of all proportion to the actual security, authentication and other measures in place to guard against malicious PDFs -- in many cases, zero.
As Microsoft knows only too well, ubiquity makes you a target. The ubiquity of PDF and Flash has brought the attention of the hackers. While the vendors adjust, prudent IT managers should review their options. The 2009 IBM X-Force Report is a great place to start.
OK, so you want to stamp your document. Maybe you need to give reviewers some advice about the document's status or sensitivity. This tip from author Ted Padova demonstrates how to add stamps with the Stamp Tool along with related comments.