Sean Carroll’s ‘The Making of the Fittest‘ shows up in a number of reference lists for thinkBio; the reason is that he’s put together a wonderful compendium of topics that can make for a compelling Introductory Biology experience. They’re basically molecules whose evolutionary history and roles are interesting and well-understood. The book packages them into interesting units, and also provides a wealth of resources for an instructor wishing to make sure he/she has a sound background in the material being taught.
Topics from the book that I’ve found useful (and that appear as thinkBio exercises) include the sickle cell anemia vs. malaria, several fascinating opsin stories (loss and regain of 3rd human color receptor; adaptation of mammals to blue wavelengths in deep water; birds and UV vision), the comings and goings of pigmentation via the MC1R gene, and the anti-cancer drug Gleevec (as of 1-23-2015, this is part of a Molecular Medicine module that isn’t posted).
The above is just the subset of The Making of the Fittest that overlaps with content on this website; there are tons of other interesting stories, all targeted at revealing the molecular evidence for evolution and written in such a way as to be accessible to the thoughtful layperson. I have found it to be both an enjoyable read as well as an educational resource, both for my own learning and for assembling teaching modules.