One branch of Apologetics deals with responses to the challenges to the faith brought by Catholicism. Since one apologist for Catholicism has recently posted a list of unsound arguments that are sometimes used by those defending Catholicism, I thought I'd post a similar list that at least identifies some areas of caution for Reformed apologists addressing Rome.
1. Eschatological Identifications
Yes, it may well be that Rome should be identified with the Whore of Babylon and that the Pope is the Antichrist. Our doctrinal standards (at least those of us that hold to the same 17th century standards as they were drafted) do identify the Pope as the Antichrist, and there are good reasons for adopting this view.
Nevertheless, these arguments don't really deal with the central issue of the gospel itself. Any argument that the Pope is the Antichrist or that Rome is the Whore require one to address the issue of whether Pope preaches the gospel or not. If he does, then clearly he is not the Antichrist nor is Rome the Whore.
Furthermore, of course, outwardly at least John Paul II and the Benedict XVI (the two most prominent popes in the minds of folks these days) were relatively decent human beings. They were not like the late medieval popes. Therefore, people have a harder emotional time dealing with arguments that seem almost ad hominem (though, of course, the argument is about the office), when the popes are outwardly moral.
Also, people have tons of trouble with the fact that "anti" in "Antichrist" is a Greek root, not a Latin root, and means "substitute" or "vicar" not "opponent" as such. That, coupled with the general difficulty associated with divining the sense of prophecy caution against using the antichristian nature of the papacy (or similar eschatological issues) as a primary argument against Catholicism. It is something better left for situations where a belligerent Romanist insists on hashing it out.
2. Sexual Abuse Allegations
Yes, sexual abuse may be a real problem in Catholicism. It may even be the necessary and natural outworking of the celibate priesthood that Rome imposes. Nevertheless, again, it is not the central issue. There are occasionally good, Christian men who fall into sin. Recall David's terrible sin with Bathsheba.
There may even be a place for noting the widespread nature of the sexual abuse problem when Roman Catholics place the character of their bishopric into issue. Nevertheless, in general, the fact that there is sexual abuse in Catholicism is simply a reason not to make your son an altar boy or your daughter a nun, not a reason to repent and trust in Christ alone for salvation.
It's not a central issue, and it shouldn't be your primary argument against Catholicism. It should be something you should bring up with reluctance, and something that you should place in perspective.
3. Dates on Doctrines
Yes, doctrines within Roman Catholicism are not static and modern Catholicism's beliefs do not much resemble the beliefs taught in the Bible or believed in the early church. Nevertheless, be careful about trying to assign dates to particular doctrines.
For example, it is frequent to see on various websites a list of doctrines and dates. The dates are when the doctrine was supposedly invented. The idea is to press home to the Roman Catholic the fact that his church has made up a lot of stuff as it went along.
There are usually a few problems with these lists. Sometimes the lists are actually not what you think they are. For example, sometimes the lists are when the doctrines were defined not when they were innovated. That's an important difference. For example, in the case of transubstantiation, we may have a doctrine that is innovated in perhaps the 11th century and then defined in the 12th century (don't rely on those dates, please - they are very approximate and just intended to illustrate the general point).
A more dramatic example is the Apocrypha. The dogmatic definition that requires Roman Catholics to accept the Apocrypha comes from Trent in the 16th century, but one can find many older writers (perhaps even a millennium before) who seemingly accept the Apocrypha as inspired.
It's important to remember that a lot of things in Catholicism were the result of a gradual development over a long period of time. As such, pinning specific dates on doctrines is liable to error and can place one in an embarrassing position.
4. "The" Roman Catholic Position
Yes, there is sometimes a single Roman Catholic position on something. For example, in theory the canons of the council of Trent are "the" Roman Catholic position on Justification (and several other topics). Very often, however, there are a myriad of positions on a particular topic within Roman Catholicism. Despite all of their myths and propaganda regarding the need for unity, Roman Catholicism has an amazing amount of diversity of views on subjects that would cause denominational splits within typical "Protestant" denominations.
So be careful. Just because you yourself were a Roman Catholic doesn't guarantee that what you were taught is going to match what a Roman Catholic from Timbuktu was taught. Just because your friend who is a Roman Catholic said that Roman Catholics believe "x" doesn't make that the only view.
As a result, either deal with the declarations of the specific person you're talking to, or qualify your statements with references to sources. For example, if you want to address liberal Catholicism, identify who your source for "the Roman Catholic view" is. Likewise, if you want to go with the "Catechism of the Catholic Church" (a fairly official document) cite it as your source.
Be careful, recognizing that your Roman Catholic friend or acquaintance may be more or less familiar with his religion than you are. There are many times that I encounter Roman Catholics who either were badly catechized or simply not good learners, who have no idea what the official positions of Roman Catholicism (as expressed through the various available mechanisms) are. Other times you may discover that your friend is a canon lawyer who can explain the ins and outs of very arcane matters of church law that would be beyond the ken of the typical parish priest.
And if you got "the Roman Catholic Position" from one of Jack Chick's tracts, double-check it. Maybe he got it right, maybe he got it wrong, but quoting him as your source is not going to be very compelling for the Roman Catholic to whom you are speaking. Do a little more research and find a more detailed explanation of the issue.
Yes, everyone that is involved in apologetics with Roman Catholicism should obtain and carefully read Foxe's Book of Martyrs (link) and there may be other similarly edifying histories. However, again, the fact that Rome has slain Christians is not the primary argument against Rome. The Reformers themselves executed folks for religious crimes (such as blasphemy) and so did those Jews who followed the Mosaic law.
The question largely is whether Rome teaches the gospel or not. If Rome does, then many of those whom she persecuted in the middle ages were not Christians. More importantly, perhaps, Rome's inquisition did not target only Christians but also blasphemers, witches, Muslims, and Jews. The fact that Christians were persecuted by Rome is not in itself a primary argument for someone to become a Christian since Rome also persecuted witches.
6. Arguments You Don't Understand
There are lots of good, Scriptural arguments against Roman Catholicism. If you don't understand them, though, you have no business using them. I'll list a few:
a) "One Mediator"
If you cannot answer the objection that Christians ask each other to pray for another, you shouldn't be using the "One Mediator" argument. The argument itself is perfectly fine, and it is clear that Catholicism is against Scripture on this matter. You, however, need to carefully understand what it means to be a mediator as well as how the Roman Catholic appeals to Mary, Angels, and the Saints violate the Scriptures.
b) "Call No Man Father"
If you cannot answer the objection that Christians call their birth fathers "father," you shouldn't be using the "Call No Man Father" argument. The argument itself is a perfectly fine one against the use of the title "Father" for every priest, but only if you understand the relationship between the injunction and the Roman Catholic usage of the term "Father" as a title.
c) "Petra not Petros"
If you cannot answer the objection that the Aramaic would not have any distinction between the two terms, you shouldn't be using the "Petra not Petros" argument. The argument itself is an acceptable argument, particularly if it is reinforced with more direct grammatical arguments (for example, Petra not se). Furthermore, the objection from a speculative Aramaic source (whether from a claim that conversation was in Aramaic, or from a claim that the evangelic text was originally written in that tongue) can be easily identified as nothing more than baseless speculation. However, one has to be aware of the typical counter-arguments and why those counter-arguments miss the point.
7. Scriptures You Don't Understand
This is perhaps a variation on (6). The point here is that you need to know the Scriptures yourself before you can instruct someone else. You need to be familiar with the Word of God if you want to lead someone else to Christ by it.
I don't say this to discourage young or immature believers, but to encourage you to grow in faith and in the knowledge of the Lord. The Bible describes the Christian apologist as being armed for battle with the "whole armour of God." In that armour, the sword of the Spirit is the Word of God.
If you were going to go to battle these days, you'd hit the target range and make sure you could hit the target from at least point-blank range. In the days of swords, you'd want to hone your skills whether with stylized sports like fencing or with more practical and direct martial training.
The same is true of the spiritual warfare that we fight. Christian apologists against every false gospel must be prepared and thoroughly.
Be scrupulously honest. Not all our opponents are honest opponents. Still, we are called to be truthful in all our dealings. The fact that the other side is not (or we think they are not) does not justify untruthful or inaccurate claims from us.
Avoid arrogance. If you make a mistake, don't be afraid to admit that you erred and to correct your mistake. This will, of course, damage the patina of perfection that you had going for you, but it is the better course of action.
I'm not saying you have to grovel, but simply admit your mistakes and move on. Learn from the experience, and remember that you are merely a human being who can and does err. Maybe your honesty will win over your opponent, maybe it will lead him to mock you. You cannot control that, but you can maintain your own integrity by correcting your mistakes.
10. Church History
The history of Christianity is not simple. Roman Catholicism certainly sometimes tries to portray it as simple. Sometimes apologists who deal with Roman Catholics try to portray it in simple but opposite terms. Don't fall into that error.
I'm not suggesting we cannot argue from church history. Rather, I am suggesting that one should approach church history with caution, as well as with a mind that church history is not our rule of faith: scripture is.
There are certain general statements that can be made about church history. As with most ares of history, however, there are numerous complexities. This is illustrated by several points:
a) Diversity Amongst the Church Fathers
On a lot of topics there was immense diversity both among the early Christian writers in general and even among those that are viewed as "church fathers." If you say, "No one ever believed 'x'" - you may quickly find yourself facing some obscure quotation from a "saint" that you never heard of before.
b) Development of Individual Fathers
Like all Christians should, many of the church fathers grew in their knowledge of God throughout their life. Accordingly, one sees some fathers (Augustine is a notable example) retracting explicitly or implicitly positions that they had held earlier in life.
As with many of us, the battles they faced inform and alter their perspective. We are much more cautious talking about the atonement in view of the Remonstrant controversy now than the Reformers were before then. The same is true of the caution that various major controversies provoked during church history.
c) Paucity of Data
There is a scarcity of patristic data, even though the works of the Greek and Latin fathers can fill almost 400 volumes in Migne's patrology. Many fathers have left only a few works behind. Other fathers have left many works behind, but have also been subjected to forgery by pseudonymous urchins, which have attempted to promote their own works under the name of a more famous writer.
Furthermore, even where the works are genuine there is often suspicion or even proof that the works have been subject to interpolation by later authors. Ignatius' works are famous in this regard, but others are not immune from this problem.
Oftentimes as well, there is a gigantic gap in the textual transmission of these early Christian writers with the earliest copy of a given work sometimes being a full millennium after the death of the author. These gaps in the transmission make tracking down the original text much more difficult.
Finally, of course, there are numerous writers whose works have been lost for a variety of reasons. For example, works that spoke out against the idolatry of icons were intentionally destroyed in the 8th century. Likewise, most of Nestorius' works have been similar lost. We also see Jerome's opponents on a variety of topics represented only in the extant works of Jerome, with their own works being lost in time.
11. False Ecumenism
For whatever reason, some folks seem to think that they will be in a better position to witness to Roman Catholics if they tell the Roman Catholics that they accept them as Christian brethren. This is just bad thinking.
If you think Roman Catholics are your Christian brethren, why are you witnessing to them? Why are you bringing them the gospel if you think they already have it? I understand that such an ecumenical statement may help lower defenses, but it really is inconsistent with your evangelical purpose.
After all, the only folks that need a physician are those who are sick. If you go around telling people that they are well, they're not going to be offended by you, but they're also not going to seek a doctor.
That's not to say that everyone who is currently affiliated with the Roman Catholic church is consequently unsaved. After all, as I've noted above, there is great diversity within Catholicism, and it is possible for those within Catholicism to read the Scripture and believe on the Lord Jesus Christ alone for salvation.
That gospel of salvation by grace alone through faith alone in Christ alone, however, is not the message of Catholicism. It should not, therefore, be one's default position that those within Catholicism have the gospel, and it is foolish (on our part) and dangerous (to their souls) for us to treat Roman Catholic apologists as though they were our brethren: in defending the gospel of Rome against the gospel of Christ they are giving strong contrary evidence of grace in their heart.
A friend of mine put it this way, with which I agree:
Our regard, generally speaking, of the lost condition of Romanists is (contrary to their complaints) a judgment of charity, because it exhibits a concern for their never-dying souls, and should always be kept in mind in dealing with them. This regard for their lost condition is not because we bear them animosity, but because we care for their souls.
We must be ready always to give an answer (to every man that asks us) a reason of the hope that is in us. We must do so with meekness and fear, having a good conscience. We must arm ourselves with truth, with righteousness, with the gospel of peace, with the shield of faith, and the sword of the Spirit: the Word of God.
We must always pray, both for the salvation of the lost and for strength in the battle for ourselves. Pray also for us, brethren, who are actively engaged in boldly proclaiming the gospel to those who need to hear it. If Paul needed prayer to boldly proclaim the gospel, we certainly need it as well.