On Lack of Intermediate Forms:
But during the process of modification, represented in the diagram, another of our principles, namely that of extinction, will have played an important part.  As in each fully stocked country natural selection necessarily acts by the selected form having some advantage in the struggle for life over other forms, there will be a constant tendency in the improved descendants of any one species to supplant and exterminate in each stage of descent their predecessors and their original parent.  For it should be remembered that the competition will generally be most severe between those forms which are most nearly related to each other in habits, constitution, and structure.  Hence all the intermediate forms between the earlier and later stages, as well as the original parent-species itself, will generally tend to become extinct.  
(On The Origin Of Species, pg 103)

On The Arbitrary Ontological Commitments Of Species-Level Creation: 
He who believes in the creation of each species, will have to say that this shell, for instance, was created with bright colors for a warm sea; but that this other shell became bright-colored by variation when it ranged into warmer, shallower waters.  
(On The Origin Of Species, pg 113)

On The Failure Of Explanation Of Species-Level Creation:
It is difficult to imagine conditions of life more similar than deep limestone caverns under a nearly similar climate; so that on the common view of the blind animals having been separately created for the American and European cavers, close similarity in their organization and affinities might have been expected; but, as Schiodte and others have remarked, this is not the case, and the cave-insects of the two continents are not more closely allied than might have been anticipated from the general resemblance of the other inhabitants of North America and Europe. 
(On The Origin Of Species, pg 117)

When we see any part or organ developed in a remarkable degree or manner in any species, the fair presumption is that it is of high importance to that species; nevertheless the part in this case is eminently liable to variation.  Why should this be so?  On the view that each species has been independently created, I can see no explanation.  But on the view that groups of species have descended from other species, and have been modified through natural selection, I think we can obtain some light…. When a part has been developed in an extraordinary manner in any one species, compared with the other species of the same genus, we may conclude that this part has undergone an extraordinary amount of modification….  An extraordinary amount of modification implies an unusually large and long-continued amount of variability, which has been continually been accumulated by natural selection for the benefit of the species.  But as the variability of the extraordinarily-developed part or organ has been so great and long-continued within a period not excessively remote, we might, as a general rule, expect still to find more variability in such parts than in other parts of the organization.  
(On The Origin Of Species, pg 128,129)

On The Imperfections Of Nature:
As Professor Owen remarked, there is no greater anomaly in nature than a bird that cannot fly; yet there are several in this state. 
(On The Origin Of Species, pg 114)

On The Rarity Of Specie Persistence:
…species very rarely endure for more than one geological period.  
(On The Origin Of Species, pg 129)