On reading The Origin of Species: Ch. 6 - Difficulties on Theory

Here Darwin points out the main attacks on the theory of natural selection. He lists four main arguments - and they are arguments that creationists, and indeed some others, still use today.

1. "Why, if species have descended from other species by insensibly fine gradations, do we not everywhere see transitional forms?"
2. "Is it possible that an animal [with one set of habits] ... can be formed by modification of some animal with wholly different habits?"
   
3. "Can instincts be acquired and modified through natural selection?" For instance those of bees to make honeycomb.
4. "How can we account for species, when crossed, being sterile and producing sterile offspring, whereas, when varieties are crossed, their fertility is unimparied?"

He deals with 1) and 2) in this chapter, and devotes a chapter each to 3) and 4).

For 1) he basically suggests two methods of isolation, and notes that both methods will tend to favour those animals more suited to the particular environments...and thus the parent species, which tend to be less well suited become less numerous and die out. The two methods are by geological change - e.g. islands being formed where once there was continuous land, and by habitat specialisation - where a species extends over a large area, and where that are covers two distinct types of habitat - while the animal is expanding over the two habitats it might remain fairly homogeneous, but once specialisations for the two habitats begin to emerge, the original, more generic variety will dwindle in numbers, and because it dwindles in numbers is less likely to produce variations that make it more successful than the more numerous, already-specialised varieties.

It is also here that he makes his oft-misquoted comment about the eye "I freely confess that it is absurd in the highest degree to suppose that the eye was formed by natural selection". He then goes on to list the possibilities.

He also makes a couple of interesting statements:
He who will go thus far, if he find on finishing this treatise that large bodies of facts, otherwise inexplicable, can be explained by the theory of descent, ouht not to hesitate to go further, and to admit that a structure even as perfect as the eye of an eagle might be formed by natural selection, although in this case he does not know any of the transitional grades. His reason ought to conquer his imagination; though I have felt the difficulty far too keenly to be surprised at any degree of hesitation in extending the principle of natural selection to such startling lengths.

and

We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. Numerous cases could be given amongst the lower animals of the same organ performing at the same time wholly distinct functions [...or...] Two distinct organs sometimes perform the same function in the same individual.

Whereby he shows the folly of letting the limits of your imagination be the limits of your reasoning. "Because I can't imagine it is so, it must not be so."