SketchBio - uses game controllers to animate and dock proteins
This is where you get the molecules to use in the viewer software.
Open-source alternative to Poser, for human 3D needs. Apparently creates cleaner meshes than Poser, too.
Moovly is a free online application to create animated videos and other multimedia content without being an expert: explainer videos, animated presentations, whiteboard videos, animated infographics, music videos, event animations… Moovly is an easy do-it-yourself (DIY) animation and video maker for everyone who’s not a multimedia professional.
This web resource presents an organized directory of cell and molecular animations, as well as a collection of original tutorials for life science professionals learning 3D visualization.
Discovery Studio Visualizer - "a commercial-grade graphics visualization tool for viewing, sharing, and analyzing protein and modeling data" - I've used this program at all my medical animation studios. Not especially user-friendly, but pretty powerful stuff for free. Does require registration to download; haven't received newsletters or obvious spam due to registration (yet).