Perhaps the best thing I can say about Intelligent Design Theory (ID for short) is that it makes for good debate. Having said that, it is important to note that the current incarnation of ID theory is essentially the same as that of William Paley. His book, Natural Theology; or, Evidences of the Existence and Attributes of the Deity (1809) put forth the same argument that Michael J. Behe does in Darwin's Black Box: The Biochemical Challenge to Evolution (1996).

This is not to say that the idea is bad because it is old; rather, it is to say that if one can make a convincing case that one is bad, one can also say the other is. I define bad in this case as not useful for its intended purpose. Both Paley and Behe are not out to add to the storehouse of science knowledge. Instead, for whatever reason, both are out to show that the existence of God can be demonstrated using empirical evidence. This can be shown to be bad for religion and for science and fails in its intended purpose--at least logically. ID theory appears to be gaining much ground through political means.

An interesting digression on this point is that ID theory is really just another form of the Doubting Thomas argument. Here is the context:

"The other disciples therefore said unto him, We have seen the Lord. But he said unto them, Except I shall see in his hands the print of the nails, and put my finger into the print of the nails, and thrust my hand into his side, I will not believe." John 20:25, King James Version.
The ID theorist is clearly like Thomas in this context, because the converse of the ID argument--that empirical proof of God is possible--is that ID theory needs the proof in question in order to support the claim that God created life. ID theory is holding up blood clotting cascades, bacterial flagella, and vesicular transport systems as the "print of the nails" constituting evidence of God. In that sense, ID theory runs against those who keep their faith separate from their empiricism.

In any event, common to Paley's and Behe's works is the claim that the best explanation for biological complexity is a supernatural intelligence. For example: Paley uses the analogy to a watch needing a watchmaker due to its complexity; Behe uses the flagellum of a bacterium to show that it is an outboard motor and so, like other outboard motors, required an intelligent designer. Paley argues that apparent imperfections in living things do not argue against a designer; Behe does the same in his book. The list goes on, and as I have time I will add to it.

My main objection to ID theory is that it uses poor analogies, such as comparing watchmaking (a natural exercise) to the creation of life (a supernatural exercise according to the argument), and exaggerated criticisms of mainstream science to try to discredit centuries of scientific effort. Absent is any concession that even if nature can't directly create a watch, it just might have been able to allow the formation of biomolecules, then DNA, then cells, then small animals and plants, then bigger animals and plants, then animals with backbones, animals with bigger brains, mammals, and finally humans, some of whom are good at making watches.