Here are two of the more interesting specialized link collections.
www.martindalecenter.com: Martindale’s Reference Desk has an unusual collection of links with a strong emphasis on science and technology. Subject categories include cyberinfrastructure and the Internet, agriculture, livestock, engineering, astronomy, chemistry, geosciences, materials science, physics, mathematics, archeology, aeronautics, maritime, languages, and health sciences. The site also links to over 23,000 online calculators.
http://home.comcast.net/~dflawson/: Deborah Lawson’s Historical Research Page is a great site. Subject categories include many different periods of history, maps, money, weapons, clothing and accessories, transportation and travel, food and drink, etiquette, language and slang, government, law, occupations, inventions and technology, postal history, crime, sexuality and marriage, household matters, religion, medicine and illness, the military, architecture, diaries and letters, historical newspapers and magazines, and advertising.
Update, 8/12/10: Deborah Lawson’s Historical Research Page has been offline for many months now. I’m trying to find out what happened, and I’ll post if I learn anything useful. Here’s the link to the Internet Archive’s October 2007 archived version of her page. If you put your cursor over her links, you should be able to see their web addresses, but don’t be surprised if many of the links are dead.