I spotted a very interesting tidbit I did not know myself on how Google calculates organic search impressions within webmaster tools.
A Google Webmaster Help thread has a Googler explaining that a search result with sitelinks is considered one impression which has two individual listings from the same domain is considered two impressions.
For example, a search for this site returns a main result with a few sitelinks. But this is not considered several organic impressions, it is only considered one impression:
But when you have two separate results, then Google will count them as two unique impressions:
Asaph from Google said:
You get one impression for each time a URL from your site shows up in the SERP with the caveat that sitelinks are not counted as separate impressions. For example for the query "panther" I get two wikipedia results, so wikipedia would see two impressions for that query.
In the example you gave about the NYT we would count only a single impression for the top level URL and no impressions for the sitelinks. If you clicked on either the top level page or one of the sitelinks, we would count that as one click for the top level page.
Did you know that?
Forum discussion at Google Webmaster Help.