An interesting article by Brian Ogilvie on intelligent design and early modern natural theology at HNN. (HT: Rhine River) I largely agree with the gist of it, but there are three particular details on which I don't quite agree with Ogilvie's argument, or at least with the way it is formulated.
(1) "Meanwhile, design arguments had little effect on how science was actually done." As it stands, this is rather unclear; since scientists did appeal to design assumptions occasionally even up to Darwin's day (Darwin explicitly takes time to deal with some of them), it's not strictly true that it had no effect on how science was actually done. If one regards things like Cuvier's 'conditions of existence' as having their roots in earlier design argument, then it had an immense effect on the way science was done that way as well, because it was the genealogical source of a concept that survives well into Darwin's own theory. Something similar seems to go for Leibniz's theory of final causes, since Maupertuis formulated and regarded the principle of least action as a particular instance of a Leibnizian final-causes-by-way-of-pre-established-harmony. I suspect Ogilvie means something like 'they had no more than a superficial effect on how science was done'; and that's a trickier argument, since it requires distinguishing between what is essentially and what is only incidentally scientific.
(2) "Natural theology had identified design as the best proof for God's existence." All I take exception to here is the 'best', since it is a dubious claim that design arguments have ever been natural theology's 'best arguments', even for most of those who accepted design arguments. At least, it takes a very, very strong empiricism to be pushed to such a position.
(3) Ogilvie talks about early modern natural theology as if it were all Paleyan; but this is certainly not true even if we are considering only design arguments. Darwin's argument, for instance, has no effect on Whewellian design arguments -- Whewellian arguments argue from natural laws, not particular contrivances. (Ditto with Berkeleyan design arguments, for different reasons. Cartesian biological-design arguments, such as we find in Malebranche and Leibniz, depended on the thesis that animals were infinite machines; but they were never essential to any sort of Cartesian natural theology anyway.) And Darwin himself recognizes this; I'd have to look up the reference, but Darwin has a letter somewhere in which he distinguishes three sorts of things that might be called 'design' and notes that evolutionary theory only directly undercuts the most crude of them, namely, the Paleyan special-creation sort of view. The others can only be dealt with on the basis of more general philosophical considerations.
But as I said, I agree with the gist of the argument. I think the disagreements above are largely due to Ogilvie's using the term 'natural theology' in a very, very narrow sense, which wouldn't have included everything that would have been called 'natural theology' and 'natural religion' in the early modern period. In that sense, there wouldn't be much disagreement at all, since my complaint would just be that the article is misleading at a few points.