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"Alice is an innovative 3D programming environment that makes it easy to create an animation for telling a story, playing an interactive game, or a video to share on the web. Alice is a freely available teaching tool designed to be a student's first exposure to object-oriented programming. It allows students to learn fundamental programming concepts in the context of creating animated movies and simple video games. In Alice, 3-D objects (e.g., people, animals, and vehicles) populate a virtual world and students create a program to animate the objects."

I have used and have seen this used. It is like a PowerPoint but web based. Presentations can be embedded.

Zooburst is a digital storytelling site. Users can make a 3-D pop-up book.

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Collection of Google Earth files to view recreated 3-D models of buildings from the American Civil War ( like Fort Sumter ).

There is no dearth of good 3D modeling software in the market but usually all of them cost an arm and a leg. Sculptris is a free 3D modeling program that offers you the same thing free of cost. Once downloaded, this free software lets you create 3D models and customize them using tons of features.