I definitely enjoyed reading Charles Darwin's The Origin of Species (Several times, indeed, at different stages of my career). Besides being one of the most influential books in Biology I always recommend its reading because is a great example of how a unifying theory is built. Indeed, the book transpires the process of thought of the author, from facts, to hypotheses, to weak points, and, therefore, is a much better example of how the phylosophy of Science works than the condensed pieces of scientific results that we digest in our daily readings of journals.
Thanks to the efforts of several institutions we are now much closer to getting the whole picture of how Darwin came about his theory. You probably all know by now that a comprehensive collection of notebooks from the british scientist is
avaliable online. Now, we will also have public access to a digital version of 330 of the 1480 titles of
Darwin's personal library. Thus, we can now read the books that Darwin used to read. Of note, full transcriptions of his annotations and marks in those books are provided. Besides the broadly acknowledged books from Lyell, and Malthus, I am sure many others may provide hints on how the theory emerged in Darwin's mind.