The following are important books I would recommend to anyone studying theology and apologetics:
Learn New Testament Greek, John H. Dobson (This work is touted as being one of the best introductions to Greek available. It's relatively short being 313 pages but is very helpful with a great easy approach).
Holy Scripture: The Ground and Pillar of our Faith (3 Volumes), David King, William Webster (Probably the finest set on the doctrine of Sola Scriptura. Some parts are a little technical but for the most part it is approachable to both the scholar and the layman. You have a Biblical defense of Sola Scriptura and a refutation of Roman Catholicism's position on Scripture and Tradition. You have a detailed discussion concerning the early church's view which shows Sola Scriptura did not emerge in the Reformation. And you have a discussion on the Catholic/Protestant canons of Scripture plus much more).
Justification: Understanding the Classic Reformed Doctrine, J. V. Fesko (This large 461 page work affirms Justification by faith alone - the imputed righteousness of Christ. It also interacts with the New Perspective on Paul doctrines, Eastern Orthodoxy, Roman Catholicism and church history. This is one of the best works on Justification).
The New Testament Documents: Are They Reliable? F. F. Bruce (This is a small but classic work defending the traditional authorship of the New Testament. It talks about dating, eyewitness testimony, the canon, Archeological evidence supporting the New Testament and the naturalist bias towards miracles as well. It is 135 pages).
The Roman Catholic Controversy, James White (This is a great work refuting Roman Catholicism. It presents all the main issues and interacts with them exegetically and historically. It is 268 pages and is endorsed by people like Dr. John MacArthur and Dr. Michael Horton).
Death and the Afterlife, Robert Morey (A very useful work. The standard work on the issues of eternal conscious torment, annihilationism, soul sleep, universalism, the difference between hades (Sheol) and hell (Gehenna) etc. It's 315 pages and is used in many seminaries as a textbook on the issue. It is both meticulous exegetically and important historically. It discusses the position of the early church and early Judaism as well).
New Testament Introduction, Donald Guthrie (Probably the finest introduction available. It is 1161 pages. I own the 4th edition. You have a thorough defense of traditional authorship of the New Testament interacting with and refuting many contrary positions and arguments. It discusses dating, audience, destination and place of origin, structure, contents etc. See also An Introduction to the New Testament by D. A. Carson, Douglas Moo, and Leon Morris. These are helpful when dealing with those who attack the reliability of the New Testament).
Putting Jesus in His Place: The Case for the Deity of Christ, Robert Bowman, J. Ed Komoszewski (Here you have one of the best defenses if not the best defense of the deity of Christ. It is 392 pages and it is organized in a very accessible way. It interacts with objections and provides a strong positive case for this doctrine).
Evangelical Answers: A Critique of Current Roman Catholic Apologists, Eric Svendsen (A great 247 page defense of Protestantism and refutation of Catholicism. This work deals a lot with authority: the infallibility of the church, the papacy, Scripture, tradition, unity and diversity in the Roman vs. Protestant church etc. It also discusses the Marian dogmas, the mass, and the priesthood. Highly recommended to counter many of the common Catholic arguments against Protestantism).
The Trinity: Evidence and Issues, Robert Morey (A large work dealing with the Old and New Testament evidence for the Trinity. It is very helpful with many good citations from scholars. It also deals with ancient Judaism's affirmation of a multi-personal God as well as the early church's view).
Some recommended commentaries which are helpful: The Expositors Bible Commentary, namely Volume 8 which has D.A. Carson's commentary on Matthew. New Testament Commentary series by William Hendriksen published Baker. New International Bible Commentary of the Old and New Testaments edited by F. F. Bruce. The Tyndale New Testament Commentaries, containing Donald Guthrie's on the Pastoral Epistles. Douglas Moo's Commentary on Romans.
The Shape of Sola Scriptura, Keith Mathison (An excellent work affirming Sola Scriptura and refuting both the Catholic position as well as their arguments against this Reformation principle. It also deals with the Eastern Orthodox position. This 364 page work is important with regard to the necessary distinction between solo Scriptura and Sola Scriptura).
The Legacy of Jihad, Andrew Bostom (One of the finest works proving exegetically that the Quran supports terrorism and offensive jihad. It also documents all of the major Muslim conquests and wars in history. It provides historical Muslim commentary on the Quranic war passages and Hadith's. 759 pages).
Encyclopedia of Bible Difficulties, Gleason Archer (A large work answering objections and alleged contradictions in the Bible. Very useful against atheists and Muslims who attack Holy Scripture. 476 pages).
The God Who Justifies, James White (An excellent exegetical defense of forensic or legal justification by faith alone. It interacts with Roman Catholic arguments as well. 394 pages).
The Gospel According to Jesus, John MacArthur (MacArthur's classic refutation of easy believism and a defense of Lordship salvation. 300 pages demonstrating that those God saves He changes).
The Justification Reader, Thomas Oden (A nice work demonstrating that justification by faith alone is both Biblical and historical. Oden shows a major strand of early church or patristic teaching which affirmed Sola Fide).
Justification in Perspective, Nick Needham (This work has many authors dealing with the history of the doctrine of justification. Dr. Needham's chapter is especially useful since it traces Sola Fide into the early church as well).
The Future of Justification, John Piper (A refutation of N. T. Wright's views concerning the New Perspective on Paul).
Who is my Mother?, Eric Svendsen (The best exegetical and historical refutation of the Catholic Marian dogmas. 334 pages).
A History of the Christian Church, Williston Walker (This 4th edition is 756 pages. It goes from the time of Jesus until modern times. Very helpful on many levels and very unbiased).
The Matthew 16 Controversy, William Webster (The Best historical refutation of Vatican 1's claim that their interpretation of Matthew 16 is the unanimous consent of the early church fathers. This work shows that Rome's view of Matthew 16 was actually the minority view among the fathers).
An Introduction to New Testament Christology, Raymond Brown (A good classic on what the New Testament says about Jesus' identity. There are many good arguments for Jesus' deity in here).
To get acquainted with Roman Catholicism and the arguments of their apologists: Not by Scripture Alone & Not by Faith Alone by Robert Sungenis. Fundamentals of Catholic Dogma by Ludwig Ott. Catholicism and Fundamentalism by Karl Keating. Nuts and Bolts by Tim Staples. Pope Fiction by Patrick Madrid. Upon this Rock by Steve Ray. Jesus, Peter and the Keys by Scott Butler. Where is that in the Bible? by Patrick Madrid.
The Inquisition, Michael C. Thomsett (An important work documenting the heinous torture and murder Rome has been responsible for in history. It speaks about four bloody stages of the inquisition citing many sources).
Eusebius: Church History, Paul Maier (Paul Maier's translation of the early church historian Eusebius' history of the church. Very important and useful work).
Mary: Another Redeemer, James White (An important work refuting the Marian dogmas Biblically and historically).
Reformation Sketches, W. Robert Godfrey (This work gives insight into Luther, Calvin and the historic Protestant confessions such as Heidelberg and Dort).
Papal Power, Henry Hudson (A nice Biblical and historical refutation of the papacy)
Romanism, Robert Zins (A useful work addressing most major doctrinal disagreements between Catholicism and Protestantism).
Can we Trust the Gospels, Mark Roberts (A short but pretty decent defense of the reliability of the Gospels. It is sort of liberal in certain areas but overall it should not be overlooked).
The doctrine of Justification, John Owen (A pretty technical defense of justification by faith alone. 448 pages published by Reformation Heritage Books).
Christ, our Righteousness: Paul's Theology of Justification, Mark Seifrid (Interesting and useful studies on justification interacting with the New Perspective on Paul and focusing a lot on Romans).
The Church of Rome at the Bar of History, William Webster (A historical refutation of Roman Catholicism demonstrating that their doctrines are countermanded by the patristic writers and events in the early church).
If you want more book recommendations contact me at firstname.lastname@example.org