To make the crust: In a medium bowl, mix graham cracker crumbs, brown sugar and salt. Drizzle butter over crumbs and stir until crumbs are evenly moistened with butter. Press crumbs evenly and firmly into bottom of prepared pan. Bake until deep golden brown, 18 to 20 minutes. Cool on wire rack while making filling. Do not turn off oven.
To make the filling: While the crust cools, in medium bowl, stir cream cheese with the lemon, orange and limes zests with a rubber spatula until softened, creamy, and thoroughly combined. Slowly add sweetened condensed milk and whisk vigorously until incorporated and no lumps of cream cheese remain; whisk in egg yolk. Add juices and whisk gently until incorporated (mixture will thicken slightly).
To assemble and bake: Pour filling into crust; spread to corners and smooth surface with rubber spatula. Bake until set and edges begin to pull away slightly from sides, 15 to 20 minutes. Cool on wire rack to room temperature. Cover with foil and refrigerate until thoroughly chilled, at least 2 hours.
Cut into squares and serve chilled. Will keep in the refrigerator for up to 3 days.