Speciality Deep Web Engines

Infomine – comprehensive virtual library and reference tool for academics. But I’ve found it not too useful, better engines out there.
Archive.org – Huge behemoth of media now public domain – rare books, sound recordings, video, 20 year archived images of all old websites, and free audio books! Makes my top 10 list. (and my top 3)
WWW virtual library – a listing of indexes to industries. Need to know about Architecture? Biochemical war? Zoology? This may get you there.
FindArticles.com – FindArticles has articles from about 500 periodicals with coverage back to 1998, and is completely free of charge.
Library of Congress – loc.gov  – Phenomenal digitized archives, “American Memory” especially interesting. Includes a good newspaper archive.
National Security Archive – Declassified papers and such. In their words – “National Security Archive Electronic Briefing Books provide online access to critical declassified records on issues including U.S. national security, foreign policy, diplomatic and military history, intelligence policy, and more.  Updated frequently, the Electronic Briefing Books represent just a small sample of the documents in our published and unpublished collections.”
www.osti.gov – Government research archives, if your tax dollars paid for it, the results are here. Also a huge collection of science presentation videos.
US Geologic Survey – Imagery and Maps galore. 3 portals to fetch data, EarthExplore, Glovis and Seamless. Extremely complex.  There are tutorials on how to get free aerial photos over at learninggis.com.
US National Map by USGS – The source for current geospatial data from the USGS.
http://adswww.harvard.edu/ – Physics and Astronomy data engine for academic papers
http://databank.worldbank.org/data/home.aspx  – Specialty statistical data on all kinds of subjects, from countries GDP to levels of blindness.
http://www.quandl.com/ – An awesome collection of 9,000,000 of financial, economic, and social datasets.