APTs: New term, old problem
The truth is: We don't know.
But we know (or should know) what we have that is of value. In a broad sense, we also know what kinds of harm can come to those valuables (see “confidentiality, integrity, availability, breach thereof”). We also know that we're immersed in a threat/countermeasure arms race that started decades ago when we learned that some people who use computers – shocker, I know – cannot be trusted. While it is true that more and more sophisticated techniques increasingly target applications, content and consumers of content (namely, human beings), we're well advised to come up for air just long enough to remember that attackers will use the simplest approach available to get the job done.
So let's pause for a reality check. Do we have a clear sense of what we need to protect and where it is? Do our employees know what is expected of them? Do they have our trust and confidence? Are we focused on protecting things of value from risk or harm, or are we bogged down on regulatory compliance issues?
There may come a time when the fastest swimmers are the ones with no secrets to protect at all. Until then, let's forgo the APT hysteria long enough to make sure we're doing a good job on the fundamentals.