Yeast artificial chromosomes. Most of the recombinant DNA people have made is certainly, in part, the product of human ingenuity, but they are nothing that couldn't in principle have come about naturally. And after all, Darwin never actually specified the source of variation, so even a "Flavr Savr" tomato doesn't really qualify as a counterexample to Darwinian evolution. YACs, by contrast, are objects that can be totally unrelated to their "parent" organism, and strictly a product of intelligent design.
The time may come when a large fraction of the organisms on Earth are non-evolved constructs. Discussions of their origin and development will center not on the fossil record, but on the manufacturer's specifications. At that point, evolution will rightly take the passenger seat (if never a back seat).
In case anyone is interested, the two results I thought of that violate the atomic theory of matter are the diffraction of individual atoms through multiple apertures (wherein an atom behaves as an extended wave) and the Bose-Einstein condensate (wherein a macroscopic collection of atoms loses all individual atomic identity, and interacts with the rest of the universe as a single, indivisible object).