Rinse and drain the pears; pat dry with toweling. Peel the fruit, core and then chop coarsely, into about 1/2-inch pieces.
Place the fruit in a heavy medium-size saucepan, along with the onions, raisins, ginger, orange or lemon peel, garlic, cinnamon, clove or allspice, red pepper flakes or jalapeno pepper and sugar. Stir in the cider vinegar, salt and black pepper and mix well.
Place the saucepan on medium high heat and bring to a boil, stirring well. Then, lower the heat to simmer and continue cooking and stirring the sauce for 1 - 1 1/2 hours, or until it is the consistency of thick jam and almost all of the liquid is absorbed. Make sure to stir often from the bottom of the pan to prevent it from scorching.
The chutney is ready when the pears are translucent and the mixture is thick, dark and syrupy. Pack the hot chutney into jars, cover with lids and let cool before storing in the refrigerator.