Place 36 mini muffin liners in each cup of 2 to 3 mini muffin pans. Place one miniature Wafer in the bottom of each liner.
Beat the cream cheese and the sugar together with an electric mixer. Scrape the sides and bottom of the bowl, then slowly add the milk and beat until smooth.
Very slowly beat in the instant pudding mix. Scrape the sides again and beat for 2 to 3 minutes until smooth. Spoon the pudding mixture into a large piping bag with a wide tip.
Pipe a dollop of pudding into the bottom of each muffin liner.
Peel and cut the bananas into thin rounds. Place one banana slice in each muffin cup, pressing down into the pudding. Pipe more pudding over the top and tap pans to allow the filling to settle.
Quickly toss the remaining banana slices in orange juice and drain immediately. (This will help prevent them from turning brown.) Place the drained banana slices and a miniature Wafer on top of each pie.
Refrigerate the pies for at least 2 hours before serving.