My thought is to start with something that is 21 years old, as it would be the first bottling for the baby's 21st birthday (legal age, responsible drinking and all that stuff). Or, if you go all out, a couple different 21s from different regions. A nice addition to the whisky gift would be a teddy bear for the baby to enjoy now! You might even think of two bottles: one for you and the father to enjoy now and one to enjoy with the baby in due course.
Then acquire stuff over the years that is distilled in the year of the baby's birth. Alot of these will come from independent bottlers. Of course, you're not going to see many for at least 10 years.
Remember, spirit isn't considered whisky in Scotland until it has been in cask three years.