Place an oven rack in the center position and preheat your oven to 350°F (175°C). Set out your 12-cup muffin pan and place a paper baking cup in each of the 12 cavities, pressing the liners gently so they sit flat. Move the cream cheese from the fridge to the counter now so it can soften while you work on the crust.
Add 1 1/2 cups graham cracker crumbs, 1/4 cup granulated sugar, and 1/8 teaspoon salt to a medium bowl. Stir with a fork until the sugar and salt are evenly spread through the crumbs. Pour in the 6 tablespoons of melted butter and stir until all the crumbs look damp and hold together when you squeeze a small handful.
Divide the crumb mixture evenly among the 12 paper liners, using about 2 tablespoons per cup. Press the crumbs firmly into the bottom of each liner with the back of a small spoon or the bottom of a shot glass. Bake the crusts for 8 minutes, just until they smell toasty and look set. Remove the pan from the oven and let the crusts cool completely in the pan, about 15 minutes.
Wash and dry the limes well. Zest 2 limes with a fine zester until you have 1 tablespoon of zest, avoiding the bitter white pith, and set aside a pinch of extra zest for garnish. Cut the limes in half and squeeze them until you have 1/3 cup of juice, removing any seeds. Slice 1 extra lime into thin rounds, then cut each round in half and set them aside for garnish.
Add the softened cream cheese to a large mixing bowl. Beat with a hand mixer on medium speed for about 1 minute, until completely smooth with no lumps. Pour in the full can of sweetened condensed milk and beat on medium speed for another 1 to 2 minutes, scraping down the sides of the bowl once, until the mixture is silky and uniform.
Pour in the 1/3 cup of lime juice, a little at a time, while mixing on low speed. Add the tablespoon of lime zest and the teaspoon of vanilla extract and mix just until combined. The mixture will thicken slightly as the lime juice reacts with the milk. Taste a tiny spoonful and add an extra teaspoon of lime juice if you like it more tart.
In a clean, cold bowl, pour in 1 cup of cold heavy whipping cream. Beat on medium-high speed for 2 to 3 minutes, until stiff peaks form and the cream holds its shape when you lift the beaters. Add about one third of the whipped cream to the lime mixture and stir it in to lighten the base. Gently fold in the remaining whipped cream with a rubber spatula, using slow sweeping motions from the bottom of the bowl, until no white streaks remain.
Spoon the filling over the cooled crusts, dividing it evenly among the 12 cups. For a neater look, transfer the filling to a large piping bag or zip-top bag, snip off the corner, and pipe it into each cup. Fill each liner to just below the rim so there is room for the whipped topping. Tap the pan gently on the counter to level the filling and pop any large air bubbles.
Cover the pan loosely with plastic wrap or foil, making sure the wrap does not touch the filling. Refrigerate for at least 4 hours, or overnight for the firmest texture. The cups are ready when the filling feels set and does not wiggle when you gently shake the pan.
Just before serving, pour 1/2 cup of cold heavy whipping cream and 2 tablespoons of powdered sugar into a chilled bowl. Beat on medium-high speed for about 1 to 2 minutes, until medium-stiff peaks form. Pipe or spoon a swirl of whipped cream onto each pie cup. Top each one with a half slice of lime and a pinch of the reserved lime zest, then serve cold.