Preheat the oven to 350 degrees F. Line a standard muffin pan with paper liners or lightly grease the pan with nonstick spray. Set aside.
In a medium bowl, stir together the graham cracker crumbs and granulated sugar until evenly combined.
Pour the melted butter into the crumb mixture and stir until all crumbs are coated and the texture looks like wet sand.
Scoop about 2 tablespoons of crust mixture into each muffin cup. Press the crumbs firmly into the bottom and slightly up the sides using the back of a spoon or small glass.
Bake the crusts for 5 minutes until lightly set. Remove from the oven and let cool slightly while preparing the filling.
In a large mixing bowl, beat the softened cream cheese until smooth and creamy with no lumps remaining.
Add the sweetened condensed milk and mix until fully combined and silky smooth.
Mix in the key lime juice and fresh lime zest until the filling becomes thick and creamy.
Add the egg yolks and gently mix until just combined. Avoid overmixing.
Spoon the filling evenly into the prepared crusts, filling each cup almost to the top.
Bake the mini pies for 15 to 18 minutes or until the edges look set and the centers still jiggle slightly.
Remove the pies from the oven and cool at room temperature for 30 minutes.
Transfer the pies to the refrigerator and chill for at least 3 hours or overnight for the best texture.
Top with whipped cream, lime zest, lime slices, or graham cracker crumbs before serving.