Beloved, I wish above all things - Margin, "pray." The word used here commonly means in the New Testament to pray; but it is also employed to express a strong and earnest desire for anything, Acts 27:29; Romans 9:3; 2-Corinthians 13:9. This is probably all that is implied here. The phrase rendered "above all things" - περὶ πάντων peri pantōn - would be more correctly rendered here "concerning, or in respect to all things;" and the idea is, that John wished earnestly that "in all respects" he might have the same kind of prosperity which his soul had. The common translation "above all things" would seem to mean that John valued health and outward prosperity more than he did anything else; that he wished that more than his usefulness or salvation. This cannot be the meaning, and is not demanded by the proper interpretation of the original. See this shown by Lucke, in loc. The sense is, "In every respect, I wish that it may go as well with you as it does with your soul; that in your worldly prosperity, your comfort, and your bodily health, you may be as prosperous as you are in your religion." This is the reverse of the wish which we are commonly constrained to express for our friends; for such is usually the comparative want of prosperity and advancement in their spiritual interests, that it is an expression of benevolence to desire that they might prosper in that respect as much as they do in others.
That thou mayest prosper - εὐοδοῦσθαι euodousthai. This word occurs in the New Testament only in the following places: Romans 1:10, rendered "have a prosperous journey;" 1-Corinthians 16:2, rendered "hath prospered;" and in the passage before us. It means, properly, "to lead in a good way; to prosper one's journey;" and then to make prosperous; to give success to; to be prospered. It would apply here to any plan or purpose entertained. It would include success in business, happiness in domestic relations, or prosperity in any of the engagements and transactions in which a Christian might lawfully engage. It shows that it is right to wish that our friends may have success in the works of their hands and their plans of life.
And be in health - To enjoy bodily health. It is not necessary to to suppose, in order to a correct interpretation of this, that Gaius was at that time suffering from bodily indisposition, though perhaps it is most natural to suppose that, as John makes the wish for his health so prominent. But it is common, in all circumstances, to wish for the health and prosperity of our friends; and it is as proper as it is common, if we do not give that a degree of prominence above the welfare of the soul.
Even as thy soul prospereth - John had learned, it would seem, from the "brethren" who had come to him, 3-John 1:3, that Gaius was living as became a Christian; that he was advancing in the knowledge of the truth, and was exemplary in the duties of the Christian life; and he prays that in all other respects he might be prospered as much as he was in that. It is not very common that a man is more prospered in his spiritual interests than he is in his other interests, or that we can, in our wishes for the welfare of our friends, make the prosperity of the soul, and the practice and enjoyment of religion, the standard of our wishes in regard to other things. It argues a high state of piety when we can, as the expression of our highest desire for the welfare of our friends, express the hope that they may be in all respects as much prospered as they are in their spiritual concerns.

I wish above all things - Περι παντων ευχομαι· Above all things I pray that thou mayest prosper, and be in health, και ὑγιαινειν· to which one MS. adds εν αληθεια, which gives it a different meaning, viz., that thou mayest be sound in the truth. The prayer of St. John for Caius includes three particulars:
1. Health of body;
2. Health of soul; and
3. Prosperity in secular affairs. That thou mayest Prosper and be in Health, as thy Soul Prospereth. These three things, so necessary to the comfort of life, every Christian may in a certain measure expect, and for them every Christian is authorized to pray; and we should have more of all three if we devoutly prayed for them.
It appears from the last clause that the soul of Caius was in a very prosperous state.

Beloved, I wish above all things that thou mayest prosper,.... Or succeed in all temporal affairs, in the business of life, in which he was; and as success of this sort depends upon the blessing of God, which maketh rich, it is to be wished and prayed for from him:
and be in health; that is, of body, which above all things above all outward mercies, is the most desirable; for without this, what are the richest dainties, the largest possessions, or the best of friends? without this there can be no comfortable enjoyment of either of them; and therefore of this sort of mercies, it is in the first place, and above all others, to be wished for, and desired by one friend for another. The rule and measure of this wish is according to the prosperity of his soul,
even as thy soul prospereth: the soul is diseased with sin, and may be said to be in good health, when all its iniquities are forgiven; and may be said to prosper, when having a spiritual appetite for the Gospel, the sincere milk of the word, it feeds upon it, is nourished by it, and grows thereby; when it is in the lively exercise of faith, hope, and love; when spiritual knowledge is increased, or it grows in grace, and in the knowledge of Christ Jesus; when the inward man is renewed day by day with fresh strength; and when it enjoys communion with God, has the light of his countenance, and the joys of his salvation; and when it is fruitful in every good work.

above all things--Greek, "concerning all things": so ALFORD: in all respects. But WAHL justifies English Version (compare 1-Peter 4:8). Of course, since his soul's prosperity is presupposed, "above all things" does not imply that John wishes Gaius' bodily health above that of his soul, but as the first object to be desired next after spiritual health. I know you are prospering in the concerns of your soul. I wish you similar prosperity in your body. Perhaps John had heard from the brethren (3-John 1:3) that Gaius was in bad health, and was tried in other ways (3-John 1:10), to which the wish, 3-John 1:2, refers.
prosper--in general.
be in health--in particular.