The critique by the National Center for Science Education (NCSE) of the chapter on anatomical homology in Explore Evolution (EE) begins by misrepresenting EE's treatment of the subject.  The NCSE claims that EE "never provides a clear and consistent definition of homology," and that EE "repeats the erroneous creationist canard of claiming that homology's definition is circular." Both of these claims by the NCSE are false.
First, EE provides a clear definition in its glossary: "Homologous structure: a body part that is similar in structure and position in two or more species but has a different function in each; for example, the forelimbs of bats, porpoises and humans." (p. 146)
In addition, EE's chapter on anatomical homology begins with the following:
"Why should the pig's forelimb and your own arm have the same skeletal pattern? After all, the pig uses its forelimbs mainly for locomotion--getting around the pen. You use your arms and hands for a wide range of tasks, such as catching a baseball, typing a report, or lifting a box--but not for locomotion. Many biologists before Darwin thought that these similarities (called "homologies") were due to a common plan or "archetype" But Darwin rejected this idea. Instead, he said these homologies were best explained by his theory of descent from a common ancestor." (p. 40)
So EE defines homology classically, as similarity of structure and position. Not surprisingly, the NCSE rejects this definition, in favor of the Darwinian definition of homology as similarity due to common ancestry. But the NCSE's charge that EE fails to define homology is completely unfounded.
Second, EE explains that if "homology" is redefined to mean similarity due to common ancestry, then it cannot be used as evidence for common ancestry without arguing in a circle:
"If homology is defined as 'similarity due to common descent,' then to say that homology provides evidence for common descent is to reason in a circle." (p. 49)
So it is not the Darwinian definition per se that is circular; what is circular is arguing that homology thus defined provides evidence for common ancestry. That would be equivalent to arguing that similarity due to common ancestry is due to common ancestry.
According to the NCSE, biologists do not make this obvious mistake. Yet the 1999 edition of Teresa and Gerald Audesirk's Biology: Life on Earth explains that "internally similar structures are called homologous structures, meaning that they have the same evolutionary origin," and on the very same page states that homologous structures "provide evidence of relatedness in organisms." Along the same lines, the 1998 edition of Sylvia Mader's Biology declares: "Structures that are similar because they were inherited from a common ancestor are called homologous structures;" on the same page, the book claims: "This unity of plan is evidence of a common ancestor." According to the 1999 edition of Raven and Johnson's Biology, homology refers to "structures with different appearances and functions that all derived from the same body part in a common ancestor," yet the book also claims that homology is "evidence of evolutionary relatedness." And the 1999 edition of Campbell, Reece and Mitchell's Biology contains the following: "Similarity in characteristics resulting from common ancestry is known as homology, and such anatomical signs of evolution are called homologous structures. Comparative anatomy is consistent with all other evidence in testifying [to] evolution."
Even Douglas J. Futuyma's 2005 college textbook Evolution (which the NCSE cites as an authority in this matter) makes the same mistake. Futuyma defines homology as "possession by two or more species of a character state derived, with or without modification, from their common ancestor," but in a section titled "Evidence for Evolution," he includes homology among the categories of evidence that are "more than sufficient to demonstrate the historical reality of evolution: all organisms have descended, with modification, from common ancestors." 
The NCSE claims that evolutionary biologists overcome the circularity by relying on more than one character to infer common ancestry: "Biologists do not look at only one line of evidence to infer common descent; it is the agreement of multiple lines of evidence about morphological, genetic, behavioral ecological and developmental similarity which allows that inference." Yet, as EE states, these different lines of evidence are often inconsistent with each other. In a later section of its critique, the NCSE itself actually acknowledges that there are disparities among the morphological, genetic and developmental evidence, though it attempts to explain them away. What the NCSE and other Darwinists never do, however, is question common ancestry itself. They simply assume that common ancestry is true, then they use homology to test subsidiary hypotheses based on that assumption.
Berkeley evolutionary biologist David B. Wake wrote in 1999 that "homology is the anticipated and expected consequence of evolution. Homology is not evidence of evolution."  EE quotes Wake's second sentence (p. 49), and the NCSE claims that EE misquotes him. But Wake's point is unmistakable: Homology is a theoretical deduction from Darwinism, not evidence for it.
Is this how science is supposed to work? Philosopher of biology Ronald Brady wrote in 1985: "By making our explanation into the definition of the condition to be explained, we express not scientific hypothesis but belief. We are so convinced that our explanation is true that we no longer see any need to distinguish it from the situation we were trying to explain. Dogmatic endeavors of this kind must eventually leave the realm of science." 
 National Center for Science Education. 2008. Section on "Anatomical Homology" in the NCSE critique of Explore Evolution. Available at http://ncseweb.org/creationism/analysis/anatomical-homology as of Feb. 23, 2009.
 Teresa Audesirk and Gerald Audesirk, Biology: Life on Earth (Upper Saddle River, NJ: Prentice Hall, 1999), p. 264; Sylvia S. Mader, Biology, Sixth Edition (Boston: WCB/McGraw-Hill, 1998), p. 298; Peter H. Raven & George B. Johnson, Biology, Fifth Edition (Boston: WCB/McGraw-Hill, 1999), pp. 412, 416; Neil A. Campbell, Jane B. Reece & Lawrence G. Mitchell, Biology, Fifth Edition (Menlo Park, CA: Addison Wesley Longman, 1999), p. 424.
 Douglas J. Futuyma, Evolution (Sunderland, MA: Sinauer Associates, 2005), pp. 48-49, 549.
 David B. Wake, "Homoplasy, homology and the problem of 'sameness' in biology," pp. 24-33 and 44-45 in Homology (Novartis Symposium 222; Chichester, UK: John Wiley & Sons, 1999), pp. 45, 27.
 Ronald H. Brady, "On the Independence of Systematics," Cladistics 1 (1985): 113-126, p. 117.