This page will have links to sites that I have found to be particularly interesting for learning more about history.
The Theban Mapping Project
Building pyramids turned out to be very expensive for Egyptian pharaohs, so starting in the Middle Kingdom they started to use the "Valley of the Kings," located near Thebes. The Theban Mapping Project of the valley is one of the most interesting and cool websites I've seen in a long time. See if you can find the tomb of King Tut!
http://www.thebanmappingproject.com/
The Greeks: Crucible of Civilization
Western Civilization owes much to the ancient Greeks. This website, a companion to the award winning PBS series, takes you back to 5th century BCE Athens. Explore the Parthenon, learn about Cleosthenes, Socrates, and Aspasia, and view clips of the original TV series!
http://www.pbs.org/empires/thegreeks/
Catal Hoyuk: Excavations of the Neolithic Anatolian Hoyuk
One of the oldest agricultural settlements ever discovered, this website gives you insight into the village and the current excavations.
The Pyramid of Zoser
Zoser's tomb is considered to be the first true pyramid. Here you can see a plan of the site and photos of the excavation.
Kufu Reveled
One of the history's biggest mystery involves the construction of the Great Pyramid at Giza. Using the most advanced 3D modelling software available, here is a very solid explanation of how millions of stone blocks were moved and laid in place.
http://khufu.3ds.com/introduction/
Warning! This needs a special plug-in, available here: http://player.virtools.com/downloads/player/install.asp
Also, you want to have a high speed connection before you begin to use this site.
Mapping History
One of the easiest ways to visualize the movement of history is through the use of Map. The University of Oregon's Mapping History has a number of wonderful map modules for all periods of history--from the Greeks to the Cold War.
http://mappinghistory.uoregon.edu/english/index.html