Creative Machines Lab, Cornell
One of their projects, spun off as the Endless Forms Website, allows you to "evolve" various objects (such as a screwdriver or lamp design) using a genetic algorithm through personal selection and randomly-generated variation. The goal is to iteratively design objects, and then use a 3D printer to instantiate them in the physical world. An example of this is shown below.
In more of a mass-production context, the vision of the future was put forth several years ago by Neil Gershenfeld in his book "Fab". According to this vision, tools and objects could be printed out with industrial-grade specs at any physical location on the planet given schematics stored on the internet.
While the vision presented out in "Fab" is typical Media Lab/futurist fare, there are now a number of cheap open-source solutions for 3-D printing. The key to printing complex objects is to provide a digital template for the model. This can be done using a CAD model. Fortunately, the people at MakerBot Industries have provided us with open-source software called Tinkercad and corresponding open-source hardware.
Tinkercad: CAD-based program for mocking up 3D designs for printing.
The applications are also quite interesting. Below are lock and key models that have been made using the Tinkercad software and d.i.y. hardware.
There are also some interesting applications to virtual reality research, particularly in the area of tangible computing. Tangible computing allows physical models to be placed in the context of a virtual space. For example, an architect can model the effects of wind and airflow on their building designs by placing a physical model on a digitization pad. The physical model is then integrated with a virtual model of the space, allowing for key parameters to be manipulated.
Advanced 3-D printing in the context of virtual world design would allow tighter integration between physical models and virtual worlds through iterative design and other refinements that account for real-world physics and processes.
In a related article from Maker Blog, work has been done on modeling biological phenomena, particularly things at the micro- and nano-scale. Below is an example of 3D DNA models that are used in the field of nanotechnology for scaffolding and other ultra-small structures.
The 3D DNA models above were not made using the MakerBot technology. Instead, a program called caNANOno  was used to design DNA structures using the principles behind DNA origami design. Physically, the designs are instantiated into DNA not by "printed" them out. Rather, DNA is annealed (heat, bent, and then cooled) so that it conforms to the desired shape.
Yet 3D printing can be used to better understand molecular biology. In this case, the interaction between actual molecular structures, virtual models, and physical models might be used to design new molecules for therapy and other applications using iterative design. This is an open (and seemingly fertile) area of research for both d.i.y.-minded engineers and biotechnologists alike.
 Douglas, S.M. et.al (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001–5006. Link to paper