What I usually do is with the first villagers,I give them last names...and it's in alphabetical order...the oldest last name and first name starts with A...and so far until the youngest.Then when two villagers has a baby,whichever gender it is,he/she will either have the beginning letter of the father's name or the mother's name.So if it was a boy,it will have the father's first initial in his name and the father's last name.If it was a girl,it will have the mother's first initial and the father's last name.

Do you guys know what I mean?
I think it's very easy to determine which child belongs to who or which family he/she is in.