It is customary when praying for an ill patient, Heaven forbid, to mention his mother’s name, for example, "Abraham Ben Sara." One reason given to explain this custom is that when we pray, we need to be as precise as possible, and a person’s relationship to his or her mother is more certain than the relationship to a father. Since there were people witnessing the birth who can definitively ascertain that a person is the mother’s child, whereas no such definitive claim can be made determining a person’s father, calling somebody by the mother’s name is a more precise form of prayer. Indeed, the Zohar (Parashat Lech-Lecha) notes that when King David prayed, he called himself "Ben Amatecha" – "son of Your maidservant" – rather than "son of Yishai," because his relationship to his mother was more certain.
What name should one use if he does not know the patient’s mother’s name?
The work Mehkereh Aretz (Yoreh De’a 26) writes that in such a case, one should use the father’s name. The Kolbo (141) indicates that the father’s name should always be used when praying for an ill patient, and thus if the mother’s name is not known, we may rely on the Kolbo’s view and use the father’s name. If neither parent’s name is known, then the patient is called "So-and-so Ben Hava," as we are all considered the children of Hava, the mother of all mankind.
Summary: When praying for an ill patient, he is referred to by his name and his mother’s name. If his mother’s name is not known, the father’s name should be used, and if neither parent’s name is known, then the patient is called "So-and-so Ben Hava."