Place the stock, soy sauce, and sugar in a small saucepan and heat slowly until small bubbles appear around the rim. Stir to dissolve the sugar. Remove the saucepan from the heat and add the bonito flakes. Wait 2 minutes, then add the lemon and/or lime juice. Strain the mixture through a fine-woven muslin cloth- or coffee filter-lined colander. Chill the sauce for at least 20 minutes, or refrigerate up to several days.
If the cooked noodles seem sticky or pasty, quickly rinse in cold water and drain well. Divide them among 4 shallow serving bowls. Garnish the noodles with sesame seeds and chives or scallions. Serve the chilled ponzu sauce on the side to drizzle on and toss in just before eating.
