Here's a potpourri of great sites to use with students:
The Scale of the Universe, allows you to zoom in and out from the smallest units of life to the edge of the known universe. You can also click on any item to display a pop-up with information about it.
Docsteach.org from the National Archives is a site you can use to find learning activities with primary source documents from the Archives. You can also customize these activities and create your own. The Hip-Hop of Shakespeare, a short TEDex talk video that explores what Hip-Hop has in common with both Shakespeare and Edgar Allen Poe and how these connections can help make these authors' works more accessible to students.
Online Showcase of 3-D Fossil Remains from the University of Michigan Museum of Paleontology allows you to manipulate and explore dinosaur bones onscreen just as you would a real object, zooming in on it, rotating it this way and that, and measuring it.