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General:
Rainbow Resource Center

Science:
American Science and Surplus - "an ever-changing pile of incredible stuff at unbelievable prices!"
GreatScopes - "The Best Value, The Finest Quality" Recommended by Scientific American ...and they're homeschoolers, too!
Paleontology in a Bag - Find fossil shark teeth, ancient marine shells, whale bones and much more in this kit collected from the Yorktown/Eastover formations fossil deposits in Virginia by a homeschool family from their property. Kit includes a study guide with photos for easy identification - creationist's perspective.

Art, Music:
Cheap Joe's Art Stuff - Fine art supplies
Music in Motion - "The Original Music Education & Gift Resource for All Ages"

Books:
Daedalus Books - Best publishers' overstock and bargain books available on the web, discounted from 50-90% off list price

Software & more computer/electronics:
Academic Superstore - Educational discounts on name brand software.