Roborant makes a provocative, laugh-out-loud case that if there was a Designer, he or she was none too Intelligent (maybe Richard Lawrence Cohen's "slowest student in the class"?):
Of course, we haven't even covered the silliest stuff. What is that appendix doing there? Nothing, just waiting to become infected and kill its owner. If you were designing a machine that had an oxygen metabolism and needed to take in food, would you plan to use the same passage for both functions? Yeah, that's good design. Would you naturally assume that the organ responsible for hearing would also house the mechanism of balance? If we were "intelligently" designed, why did the designer make our jaws too farking small for all of our teeth? Those "wisdom" teeth certainly don't seem like wise design.
No, the human body is a massive collection of kludges and imperfections. It works, but is subject to an awful lot of failures and chronic problems. Elsewhere in creation, the story isn't any better. Most creatures are full of design flaws. From the panda's thumb, to the vestigial wings of flightless birds, to the hip bones deep inside of whales, to the parthenogenetic lizards of the genus Cnemdophorus, nature is full of kludges, half-measures, make-dos, re-works and downright crazy adaptations.
In fact, these misdesigns are some of the strongest arguments in favor of evolution. Those tails that human embryos have, then lose, are pretty obvious signs, aren't they? What about the fetal teeth of certain whales that form, but never erupt, then get reabsorbed? Sounds like evolution to me. Those flounders that are born with an eye on each side, but then one eye moves over to the other side: evolution or intelligent design? Flightless birds which nevertheless have hollow bones to conserve weight? Maybe God just likes his penguins to have hollow bones! Nearly all of the "design flaws" I have described make perfect sense if we assume evolution as the design mechanism. Evolution finds it much easier to adapt existing structures to new purposes (horses with one hoof still have bones inside to support three toes) than to invent from scratch.
And I didn't even get to the parts about sexual anatomy! Read it and laugh, or you might cry. I don't think this rules out the operation of some kind of intrinsic intelligence on the mutation end of the process. But if so, omniscient and omnipotent it ain't.
UPDATE: This very apropos joke just arrived in an e-mail full of jokes about engineers:
Three engineering students were gathered together discussing the possible designers of the human body. One said, "It was a mechanical engineer. Just look at all the joints." Another said, "No, it was an electrical engineer. The nervous system has many thousands of electrical connections." The last one said, "Actually it must have been a civil engineer. Who else would run a toxic waste pipeline through a recreational area?"