If tomatoes are even partially ripe, peeling is recommended to avoid tough, stringy bits forming during cooking. Slice peeled tomatoes; sprinkle with salt and let stand for several hours or overnight. Drain well.
Peel, core and quarter apples and stick a clove in each quarter. Peel and slice onions, Stir in sugar, vinegar and water. Mix to combine. Bring to a boil, reduce heat and cook slowly for about 3 hours. stir often to avoid scorching.
Ladle into hot, steriized jars, leaving 1/2 inch headspace. Seal with 2-piece lids, allowing 10 minutes processing time.