To make the pasta: In a bowl or work surface, add the flour. Make a well in the center and add the eggs. Mix together to form a dough. Slowly add just enough water to make a smooth, soft dough. Wrap in plastic and set aside for 30 minutes to 1 hour.
To make the filling: In a large bowl, combine the ricotta, Pecorino Romano, and egg. Mix in the lemon zest, nutmeg, black pepper, and salt. Cover and refrigerate until needed, up to 1 day.
To assemble: Line a large baking sheet with parchment. Divide the pasta dough in half. Remove 1/2 to a floured work surface and keep the other half covered. Use a pasta machine, flouring as needed, to gradually roll out the dough to the thinnest setting. Flour the desired ravioli mold and cover with a sheet of pasta. Fill each cavity with the lemon ricotta filling. Top with another sheet of pasta and use a rolling pin to seal and cut out the ravioli. Remove and separate the ravioli and transfer them to the prepared baking sheet. Repeat with remaining dough and filling.
Bring a large pot of salted water to a boil. Reduce to medium-high heat and add the prepared ravioli in batches, being careful not to overcrowd. Gently stir the bottom and cook until they float to the top. Use a slotted spoon to gently remove the ravioli to a colander. Repeat with remaining ravioli.
Serve immediately with desired sauces or toppings.