Spotted by Enrico Altavilla, it seems Google added a 3D button to the knowledge graph results for molecules answers. Search for [sugar formula] and you'll see one of many examples:
Click on the 3D icon at the top right of the knowledge graph box and it opens up a 3D view:
Enrico explained:
1) Search on Google for [sugar formula]
2) Click the button "3D" that appears in the top box
3) Enjoy the interactive animation (move it with your mouse)
4) Search for other molecules
5) Play with carbon dioxide in full screen: www.google.com/o3d/shopping/viewer/360?q=tYcgzyDA6me
6) Find more molecules searching for this: [site:www.google.com/o3d/]
Google has had animated math graphs for a while now.
Forum discussion at Google+.