2 Timothy 1:16-18 (RSV): “May the Lord grant mercy to the household of Onesiphorus, for he often refreshed me; he was not ashamed of my chains,  but when he arrived in Rome he searched for me eagerly and found me –  may the Lord grant him to find mercy from the Lord on that Day – and you well know all the service he rendered at Ephesus.” (cf. 4:19)
Catholics pray for the souls in purgatory, in order to aid them in their journey through purgatory to heaven. In praying for the dead, it’s very reasonable to contend that an intermediate state is presupposed, because it would be futile to pray for those in hell (prayer can no longer help them) and unnecessary to pray for those in heaven (they have everything they need). This verse offers biblical support for this belief.
Protestant commentators have been hopelessly confused about the passage and cannot offer a coherent, unified testimony as to its meaning. Consulting their conflicting opinions makes for fascinating reading indeed.
The well-known evangelical Protestant work, The New Bible Commentary (3rd edition, 1970) takes the astounding position that Onesiphorus is probably dead (citing 2 Tim. 4:19), yet holds that Paul was praying for his conduct during life. The prominent Jamieson, Fausset, and Brown Commentary (1864) also holds that Paul was praying, but obviously not for a dead man because, after all, “nowhere has Paul prayers for the dead, which is fatal to the theory, . . . that he was dead.” This is circular reasoning: merely assuming what it claims is proven.
Greek scholar A. T. Robertson (Word Pictures in the New Testament, 1930, Vol. IV, 615) concedes that Onesiphorus was dead, but desperately describes Paul's prayer for him as a “wish” (a distinction without a difference). The International Standard Bible Encyclopedia (1939) makes the same (what can only be described as) rationalization, using the description, “pious wish” (Vol. IV, 2195). Famous Presbyterian commentators Matthew Henry (1662-1714) and Albert Barnes (1798-1870) casually assume that Onesiphorus was not dead, since Paul prayed for him – again making prior assumptions about what is possible in the first place, which amounts to eisegesis, or reading into Scripture notions that are not there. But John Calvin denied that he was dead.
The “game” and conundrum for all these commentaries is to refuse to accept both things together: a dead man, and someone praying for them. Thus, if they think he was dead, they deny that he was prayed for. And if they acknowledge prayer, they deny that he was dead.
But all is not lost. I have located several Anglican commentaries and a few others (thanks largely to Google Books!), that accept both factors together and state that Paul prayed for a dead man. The Anglican commentaries include Alfred Plummer (1841-1926), in The Expositor's Bible, James Maurice Wilson (1836-1931), Sydney Charles Gayford (in 1905), John Henry Bernard (1860-1927), Charles John Ellicott (1816-1905), and J. N. D. Kelly (1909-1997), in A Commentary on the Pastoral Epistles (London: A&C Black, 1963, p. 171). The latter states:
On the assumption, which must be correct, that Onesiphorus was dead when the words were written, we have here an example, unique in the N.T., of Christian prayer for the departed. . . . the commendation of the dead man to the divine mercy. There is nothing surprising in Paul's use of such a prayer, for intercession for the dead had been sanctioned in Pharisaic circles at any rate since the date of 2 Macc 12:43-45 (middle of first century B.C.?). Inscriptions in the Roman catacombs and elsewhere prove that the practice established itself among Christians from very early times.
William Barclay (liberal Presbyterian: 1907-1978) concurs in his Letters to Timothy, Titus, and Philemon. So does the well-known Reformed Protestant Church historian Philip Schaff (1819-1893) in The International Illustrated Commentary on the New Testament (1889, Vol. IV, 587). Other commentators who agree include W. Robertson Nicoll, The Expositor's Greek Testament (1951) and the renowned Henry Alford, The Greek Testament (1958).
What are we to conclude from all this jumble of various Protestant opinions? I'm always happy to present the information and let readers make up their own minds, but I conclude (for whatever it’s worth) that the passage is pretty straightforward. Therefore, when a commentator decides that Onesiphorus is not dead or that he was and wasn't prayed for, it's an example of eisegesis and letting denominational bias interfere with objective Bible commentary.
It's always ironic to note such an occurrence among Protestants, since our separated brethren are very fond of frequently pointing out that they go by the Bible alone, as their only infallible source of authority and rule of faith. They will habitually claim that they merely let it speak for itself.
Yet when it comes to an issue like this, where the biblical text seems to run contrary to a tenet of Protestant denominational dogma (i.e., that prayer for the dead is impermissible), all of a sudden there is plenty of “explaining away” and denial of what seems to plainly be present in the passage.
Bias should never surprise us. It's natural to the human mind, and we all (including Catholics) have it. We all bring prior traditions to our Bible commentary, too, no matter how much we may try to deny it. It's not a matter of “whether,” but which tradition is present.
I maintain that Catholics are as free as anyone else (if not more so) to simply let the Bible speak for itself. If it indeed teaches prayer for the dead in this passage, we accept that, as part of God's inspired revelation. It corresponds to Catholic doctrinal/dogmatic teaching, tying into purgatory. In my experience of over 26 years of Catholic apologetics, the Bible always does that. This may be little-known and frequently denied by Protestants, but it's true, and I've shown it with many examples in my own work, such as this present one.