This one is fun.
Proteopedia is a 3-D-graphic-oriented Wiki devoted to macromolecules, mostly proteins at present, of course (but hopefully that will soon change):
http://www.proteopedia.org/wiki/index.php/Main_Page
You can grip and turn the molecules freely with mouse/cursor.
It has 70K+ macromolecules (mostly proteins) so far.
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