From Wikipedia:
The deep Web (also called Deepnet, the invisible Web, dark Web or the hidden Web) refers to World Wide Web content that is not part of the surface Web, which is indexed by standard search engines.
Mike Bergman, credited with coining the phrase,has said that searching on the Internet today can be compared to dragging a net across the surface of the ocean; a great deal may be caught in the net, but there is a wealth of information that is deep and therefore missed. Most of the Web's information is buried far down on dynamically generated sites, and standard search engines do not find it. Traditional search engines cannot "see" or retrieve content in the deep Web – those pages do not exist until they are created dynamically as the result of a specific search. The deep Web is several orders of magnitude larger than the surface Web.
Now how can we (as a programmer) optimize my web sites for deep web searching?