SketchUp was used to do both of these graphics. The DNA double helix is even uploaded onto the SketchUp 3D Warehouse here. The caffeine molecule was built on top of a grainy image taken from online, then exported many times larger and with much greater quality as a jpeg to GIMP where it was finished.
The advantage to using 3D models for graphic design is that after you create it once, you can use it as an asset over and over again, from different angles, to create animations, and update dynamically using components. The Wuzhen Village animation was in fact created using a model made specifically for a logo design.
Here is a collection of images produced for the company calendar of a Netherlands-based LED light bulb manufacturer. The images were later compiled into various desk calendars for each of the countries the company does business in, including a Thai, Malaysian, and Indonesian version. This project was done using GIMP and SketchUp's Layout to produce the .pfd.