In a medium mixing bowl, combine the graham cracker crumbs, melted butter, and granulated sugar. Stir until all the crumbs are evenly coated and the mixture looks like wet sand.
Spoon about 2 to 3 tablespoons of the graham cracker mixture into each dessert cup. Press the crumbs gently into the bottom using the back of a spoon to create an even crust layer.
In a large bowl, beat the softened cream cheese with a hand mixer for 2 to 3 minutes until smooth and creamy. Scrape down the sides of the bowl as needed.
Add the sweetened condensed milk, key lime juice, and fresh lime zest to the cream cheese. Beat until the filling becomes thick, smooth, and fully combined.
Fold the whipped topping gently into the lime mixture using a silicone spatula. Continue folding until the filling becomes fluffy and no white streaks remain.
Spoon or pipe the key lime filling into the prepared dessert cups over the crust layer. Smooth the tops gently with the back of a spoon if needed.
Place the dessert cups into the refrigerator and chill for at least 2 hours or until fully set. For best results, chill overnight.
Before serving, top each dessert cup with whipped cream, lime zest, crushed graham crackers, or lime slices. Serve cold.