Example 2: reptile-mammals (part of a longer article)
Article by biochemist Douglas Theobald in the TalkOrigins Archive, looking at creationist misunderstandings about the transition.
Appendices: Science; Transitional Fossils; and Embryos
Article on the website of the National Center for Science Education (NCSE). Please scroll down to the part 'The Reptile-mammal Transition', which deals with further creationist misunderstandings about the transition.
The Mammal-Like Reptiles: A Study of Transitional Fossils
Article by James A. Hopson in The American Biology Teacher, looking at this transition and creationist claims relating to it.
The Rocks Were There: Straight Science Answers to Bent Creationist Questions
Book by James Downard and Jackson Wheat dealing with creationists' mishandling of the scientific literature relating to this topic on pages 242-247 of volume 1.
Evolution of mammalian auditory ossicles
Wikipedia provides a reasonable overview of the topic, but of course does not deal with creationist claims.