Of the list of the titles of the Pope, what does the title Holy Father mean?
Please see Other titles.
Do we also know when it was first used?
We call the Pope "Father" in the first place as a bishop. The concept of the "apostolic succession" to which the Catholic Church subscribes means that bishops are considered successors of the apostles, "those sent out" (apostoloi in Greek) by the Lord, and thus are acting on behalf of Our Father in Heaven. The Catechism of the Catholic Church, speaking of the consecration of a bishop, says that the prayer at the consecration asks God to give the bishop
As far as "Holy": The word, according to the etymology website etymonline.com, was adopted in Old English as a translation for the Latin sanctus. Apparently we don't have any pre-Christian evidence of its use, but it seems to have meant something like "that which must be preserved untouched", a fair translation of the Latin word, which meant something like "something set apart". Only God, of course, is holy in himself; but we often call people or places "holy" to express the idea of their being dedicated to, or set apart for, God. Just as we call bishops "Reverend" (that is, "he who is to be revered", or "greatly respected"), so we call the Bishop of Rome "Holy": "he who is set apart" as the leader of the Holy Church.
(While researching this, I did find an alternative answer: "Because 'Holy Frank' just sounds silly.")