PDF exploits—mostly targeting Adobe Reader and Acrobat programs—are very commonly used on drive-by web sites. This situation is probably the result of the widespread use of the Adobe plugin, a rather large of number of vulnerabilities found in it, and reliable exploitation techniques.
The analysis of malicious PDF files is often complicated by the use of various obfuscation (or better, “confusion”) techniques. In particular, malicious PDF files are often malformed: expected sections are missing entirely, others are truncated. The attacks are still successful because Adobe Reader does a good job at automatically repairing the damaged file. Of course, analysis tools are not necessarily as good at that.