Starting with John Owen, the following works stood out:
Biblical Theology
Display of Arminianism (1642)
Doctrine of Justification by Faith (1677)
Doctrine of the Saints’ Perseverance Explained and Confirmed (1654)
Evidences of the Faith of God’s Elect (1695)
Indwelling Sin in Believers (1667)
Vindication of the Doctrine of the Trinity (1669)
How We May Bring Our Hearts to Bear Reproofs (1676)
Edit: I got the list from this site:
John Owen » Works