This is by no means an exhaustive list, nor is it intended to be a list of my favorite books in general, rather these are titles which have been especially helpful in forming my understanding of Biblical discipleship. I will be adding to the list periodically as other titles come to mind.
The Master Plan of Evangelism by Robert Coleman is the one book I have used the most in teaching others how to make disciples. It is a straightforward discussion of how Jesus went about making disciples, and as such, it is immensely practical and timeless. See an excellent review of this book here.
The Divine Conspiracy by Dallas Willard is a more academic and philosophical treatise on the process of discipleship (and thus a bit harder to digest), focusing on Jesus’ Sermon on the Mount. In Willard’s “Curriculum for Christlikeness” (chapter 9) he describes what he calls “the golden triangle” of spiritual transformation, which has become a foundational model for me in understanding how God changes our hearts in Him.
A Praying Life by Paul E. Miller is not a book on discipleship, but on prayer. But what he describes and illustrates in this book is a life of dependence and trust in our God, thus without directly teaching principles of discipleship, he is nonetheless creating a very practical, down-to-earth picture of discipleship in the midst of everyday life.
Spiritual Disciplines Handbook by Adele Ahlberg Calhoun is a wonderfully useful tool to help us engage with God through various types of practice and training (i.e. spiritual disciplines). It is truly a “handbook”, not a textbook, so it is not designed to be read straight through, but rather to be taken with you on retreat and brought into your prayer closet to help facilitate your process of “training yourself for the purpose of Godliness” (I Tim. 4:7).