Tamar tipped me off to people seeing secondary search boxes in the Google search results. I see them myself now. For example, a search on amazon returns this search box directly under the snippet but above the URL; here is a picture:
It also works for a search on wikipedia:
And even for ny times, which also has Sitelinks.
When you type a keyword into the search box and click search, you are essentially searching the site via a site command using Google’s search engine. For example, I typed in mortgage rate into the search box within my NY Times search and Google returns pages from the New York Times that match that query.
Postscript: Google has now made an official announcement about this. See Google Debuts “Search Within A Site” Search Box Feature.