Cut 4 shallow slits lengthwise through skin of each apple. In saucepan large enough to fit apples in single layer, bring sugar, water (2 cups), wine, vinegar, cinnamon, allspice, thyme and salt to boil, stirring until sugar is dissolved. Add apples; reduce heat and simmer, turning occasionally, until apples are tender, about 40 minutes. With slotted spoon, transfer apples to dish.
Meanwhile, peel cipollini (onions), leaving base intact. Add to saucepan; simmer until tender, about 20 minutes. With slotted spoon, add to apples.
Discard thyme. Increase heat to high and boil until consistency of maple syrup, about 10 minutes. Pour over apple mixture. (Make-ahead: Cover and refrigerate for up to 24 hours; if desired, reheat to serve.)