Search re-targeting is a prospecting buy – it finds those individuals who have searched for relevant terms on Google, Yahoo! or Bing and targets them with display ads.
Site re-targeting refers to targeting individuals who have visited your site and then left, often without completing the action you want them take. It talks exclusively to those individuals who have already visited, and so is a double investment in the same audience.
The two work very well together: search re-targeting for prospecting, and site re-targeting for increasing conversion rates.
