Unlike pages on the visible Web (that is, the Web that you can access from search engines and directories), information in the Deep Web is just not visible to the software spiders and crawlers that create search engine indexes. Since this information makes up the vast majority of available content on the Web, we are potentially missing out on some pretty amazing resources.
However, that's where Deep Web search engines, tools, and directories come in. There are many Deep Web search tools that you can use to dive into this wealth of information, as you'll see from the following list.
Clusty is a meta search engine, meaning it combines results from a variety of different sources, filtering out duplicates and sifting the best content that you might not have seen otherwise to the top of the search results.
More about Clusty
SurfWax gives you the option to grab results from multiple search engines at the same time. You can also create SearchSets, your own personalized sets (lists) of sources that you save and use over and over. SurfWax is a good tool for delving into the Deep Web since it retrieves information you won't be able to find with other search engines.
More metasearch engines
The Internet Archive is an amazing database offering access to movies, live music, audio, and printed materials; plus, you can look at older, saved versions of nearly every site ever created on the Internet - over 55 billion at the time of this writing.
Scirus is a science search engine dedicated to only searching science-specific content. At the time of this writing, Scirus searches over 370 million science-specific web pages, including scientific journals, scientists' dedicated homepages, courseware, pre-print server material, patents, and much more.
More science resources
USA.gov is an absolutely mammoth search engine/portal that gives the searcher direct access to a wide variety of information and databases from the United States government, state governments, and local governments. This includes access to the Library of Congress, an A-Z government agency index, the Smithsonian, and much, much more.
More government resources