Set a fine-mesh strainer over a heatproof, medium bowl. In a heavy, medium saucepan, whisk together the sugar, citrus juice, eggs, egg yolks and 2 tbsp. citrus zest. Add the butter and cook over medium heat, stirring, until completely melted.
Lower the heat to medium-low and cook, stirring constantly, until the mixture thickens, 6 to 8 minutes (do not let it boil). Strain, discarding the solids. Stir in the remaining 1 tbsp. citrus zest. Press a sheet of plastic wrap directly onto the surface. Let cool to room temperature, then refrigerate for at least 4 hours.
Bake the phyllo cups according to package directions; let cool. fill them with the citrus curd and collop each with whipped cream. Top with more zest if desired.