One frequently employed argument against the theory of intelligent design is that if living things are indeed the product of intelligent agency the designing agent must not be all that competent since some biological structures appear to be quite poorly designed.
The argument goes back at least to David Hume (d. 1776) in his Dialogues Concerning Natural Religion, and modern skeptics point to the human eye as an almost paradigmatic illustration of Hume's claim. The light sensitive cells in the eye, it has long been thought, are facing the wrong way in the retina.
Yet, as research on the eye continues it looks more and more as though the eye is, in fact, optimally designed for the role it plays in vision.
Here's a short video which makes this point quite well:
The optimality of the eye's design coupled with the fact that complex eyes have been around since the cambrian and have no fossilized ancestral predecessors, leads to the conclusion that this very complex structure arose with relative suddenness in the history of life and apparently de novo.
That's pretty hard to explain on any naturalistic theory of origins.