Has the CEO of your company ever freaked out after a few keywords suddenly vanished, convinced the business will go down in flames if this magical phrase drops out? Of course, you've already provided data that shows most of the traffic comes in from the long tail, but now you need to come back in with specific reports that ensure that there's little to no decrease in traffic.
Let's look at a few things you should check to make sure all things are working appropriately, including site latency due to overtaxed servers, poor server configuration, or changes to various elements of a site or marketing efforts.
First, how fast is your site performing? Was there a sudden increase in latency on your site? Latency can cause severe repercussions when it comes to ranking for highly competitive terms.
Imagine if you want to rank for the keyword "cars." This keyword most likely receives more than 200,000 searches per day. If you're on a shared Web hosting service, one that's likely hosting more than 200 other sites, your likely response rate is two to three seconds.
For example, my blog is on a hosted environment and can commonly take longer than two seconds to bring up a simple static article -- not the greatest user experience normally found. This is amplified when multiple queries at the same time are introduced to a server that may not be configured correctly, or is incapable of responding adequately.
Is it possible that there might be a break between the front and back end database servers? These backups, or queuing to retrieve data, will commonly cause a server error known as a 500 (server busy). Servers commonly return this message when it's configured incorrectly, usually in a surge for minutes at a time.
This period of time usually isn't enough to show up within Google's Webmaster Tools. I've seen months of such issues without a single reported error. This is a common problem on many large sites that I've audited and reviewed.
What else could have been tinkered with? Could the hosting environment have changed? One major factor that can have devastating instant effects is moving to a new IP address range outside of the country's normal range. This resets many filters that are used by engines such as Google and can wipe out ranking in one quick swoop.
Another consideration: has your business development team actively recruited new partners to display your products and or content in a syndicated fashion?
Also, if your site is just a couple years old and your content is replicated to a site, maybe one that is seven years old with a major history of high rankings and strong search engine rankings, it's possible that an algorithm patented by Google could transfer such ownership to the strongest site. The exact workings of this feature aren't known; older content may not move in terms of credit to another site. However, I've seen this happen several times.
Make sure that appropriate credit, in terms of backlinks, is always assigned. Never allow these links to be either nofollowed or hidden behind redirected URLs that can't be crawled. You'll never get the credit in order to block such actions from hurting you.
Long story short: check the details, you may uncover a simple answer that may not be so simple to correct.