In Joel Beeke’s Reformed Confessions, he provides an extensive bibliography with recommendations.  His favorite books by topic are listed below:

• The Doctrine of God: Knowing God by JI Packer
• Inspiration of Scripture: 2 Timothy 3:16, 2 Peter 1:21, Thy Word is Truth by Edward Young and Nothing but Truth by Brian Edwards
• Canon of Scripture: Inspiration and Canonicity of the Bible by Laird Harris
• Authority of Scripture: Authority by Martyn Lloyd-Jones
• Scripture’s Sufficiency and Inerrancy: Bible Inerrancy Primer by John Gerstner
• The Trinity: The Trinity by Edward Bickersteth
• Deity of Jesus: The Gospel of John and A Primer on the Deity of Christ by John Gerstner
• Deity of the Holy Spirit: The Doctrine of the Holy Spirit by George Smeaton
• Creation: Studies in Genesis One by Edward Young
• Angels: The Ministration of, and Communion with Angels in The Works of Isaac Ambrose
• Devils: Satan Cast Out by Frederick Leahy
• Providence: The Mystery of Providence by John Flavel
• Human Creation: Man: The Image of God by Gerrit Berkouwer or at a more popular level The Christian View of Man by Gresham Machen or Knowing Man by JI Packer
• Fall: Human Nature in its Fourfold State by Thomas Boston
• Bondage of the Will: The Bondage of the Will by Martin Luther
• Original Sin: Original Sin in Volume 3 of The Works of Jonathan Edwards or An Unregenerate Man’s Guiltiness Before God in Respect of Sin by Thomas Goodwin
• Predestination: John 6:37-44, Romans 9-11, Ephesians 1, Calvin’s Institutes 3.21-24 and The Reformed Doctrine of Predestination by Loraine Boettner
• Salvation Promises of God: The Wells of Salvation Opened by William Spurstowe (out of print)
• Messianic Promises: Christ Revealed by Thomas Taylor or at a popular level The Unfolding Mystery by Edmund Clowney
• Recovery of Fallen Man: Christ our Mediator by Thomas Goodwin
• Incarnation: The Virgin Birth of Christ by Gresham Machem
• Christ’s Two Natures: Chalcedonian Creed and The Person of Christ by Loraine Boettner.  At a deeper level, The Person and Work of Christ by BB Warfield
• Justice and Mercy in Christ: Heidelberg Catechism questions 9-18 and The Commentary of Dr. Zacharias Ursinus on the Heidelberg Catechism
• Christ’s Sufferings: The Suffering Savior by Fredrich Krummacher or one volume When I Survey by Herman Hoeksema.  For the last week of suffering, The Passion of Our Lord by Erich Kiehl
• Christology: Christ All in All by Philip Henry
• Christ as High Priest: The Work of Christ by Robert Letham
• Christ’s Atonement: The Orthodox Doctrine Regarding the Extent of the Atonement Vindicated by Charles Hodge or popular Vicarious Atonement Through Christ by Louis Berkhof
• Salvation by Faith Alone: The ABC of Faith by Alexander Comrie
• Justification: An Inquiry into the Nature of God’s Act of Justification in The Works of Thomas Halyburton or Faith Alone by RC Sproul
• Sanctification and Holiness: God’s Way of Holiness or Holiness by JC Ryle
• The Ceremonial Law: Institutes of Elenctic Theology V2 Chapters 24-25 by Francis Turretin
• Christ’s Intercession: The Knowledge of Christ Glorified by John Hurrion
• The Doctrine of the Church: The Glorious Body of Christ by RB Kuiper and Calvin’s Institutes Book 4 Chapter 1.  For the most extensive treatment see The Church of Christ by James Bannerman
• Church Membership: The Duty to Join the Church and to Remain with Her in The Christian’s Reasonable Service by Wilhelmus a Brakel
• True and False Church: The Christian’s Reasonable Service by Wilhelmus a Brakel
• Church Scandals and Heresy: A Treatise Concerning Scandal by James Durham or Concerning Scandals by Calvin
• Church Governance: Biblical Church Government by Kevin Reed
• Church Offices: Order in the Offices by Mark Brown
• Homoletics: The Art of Prophesying by William Perkins
• Pastoral Theology: The Reformed Pastor by Richard Baxter
• Elders: The Problem of Eldership and Its Wider Implications (Banner of Truth #395-396d)
• Church Order: Paradigms in Polity by David Hall and Joseph Hall
• Worship: A Fresh Suit Against Human Ceremonies in God’s Worship by Williams Ames or Gospel Worship by Jeremiah Burroughs
• Church Discipline: Handbook of Church Discipline by Jay Adams
• Sacraments: Institutes Book Two
• Church and State: City of God by Augustine and The State in Its Relations to the Church by William Gladstone
• The End: Revelation and Behold He Cometh by Herman Hoeksema
• Heaven and Eternity: The Saints’ Everlasting Rest by Richard Baxter and The World to Come by Isaac Watts