For a friend's birthday last night, we made cookies (below) using a custom cookie cutter we bought from an online service. They came out well, but I ended up wanting more control over the process.
Next time, I'll use Cookie Caster, the free service that lets users make their own cookie cutters and download the digital files to their own 3D printer. Most everyone can scare up a 3D printer these days, either from a friend or at school. Doing it ourselves would have given us the chance to iterate on the baked good until it looked perfect. Owning more of the process, we could have done two cutters and experimented in final dough form.
Cookie Caster is a free service (it doesn't offer cookie cutters, only digital files). It launched last fall, and it grew out of the Noisebridge hacker space in San Francisco. You can also create cookie cutters by uploading your own image and tracing around it:
To make the multiple cookie cutters needed to create versions of these cookies from Fancy Flours (below), you might need something like Autodesk 123D Make or improvise your own slices. Not sure if Cookie Caster could help envision a 3D cookie like this.