Second Story (http://www.secondstory.com):
Yin Yu Tang: http://www.pem.org/yinyutang/
Thebian Mapping Project: http://www.thebanmappingproject.com/
A More Perfect Union: http://americanhistory.si.edu/perfectunion/experience/index.html
Remembering Pearl Harbor: http://plasma.nationalgeographic.com/pearlharbor/
(Many others; go to their main site and click on "Projects")

Others:
New York and Los Angeles Dynamic Maps: http://histmaps.research.cuny.edu/dynamic_maps.htm
Catlin's Indian Gallery: Campfire Stories (Smithsonian): http://catlinclassroom.si.edu/
Devices of Wonder (Getty): http://www.getty.edu/art/exhibitions/devices/choice.html
Zoot Suit Culture (PBS): http://www.pbs.org/wgbh/amex/zoot/eng_sfeature/sf_zoot_mx.html
Without Sanctuary: http://www.musarium.com/withoutsanctuary/
Flash Film Festival Awards 2004: http://www.flashforward2004.com/peopleschoice.asp
Virtual Knee Surgery: http://www.livingchildren.com/knee/