This refers to web pages which are not indexed by search engines and directories; a more valid term of the Deep Web would probably be the "Invisible Web".
For a search engine to find a website, the website either has to have a hyperlink pointing to the address from a website which is currently indexed and crawled by the search engine, or has to be submitted to the search engine via it's submission tool. If neither of these things are done by the website owner, then there is a good chance the site will not be indexed and will be largely invisible to users on the World Wide Web.
Alongside a website owner simple not submitting his website for submission to a search engine, there are a number of other reasons why a website may enter the Deep Web.
1. Websites that use scripts to generate new pages. These pages can have URLs that search engines cannot read; therefore, this data is not crawled and indexed by a search engine.
2. A website has content which contravenes the rules of search engines and is therefore banned from them and no longer indexed or crawled.
3. Websites which requires membership; this usually means a password and username is required to access the website, which usually means it blocks search engine crawlers.
4. Content uploaded in non-textual form; a prime example would be a flash file: most search engines can not access and read the data upon it.
5. Any type of procedure which requires a user to enter a manual code/calculation to view content: this again will more than likely block access to search engines.