Toss shallots with oil and minced fresh thyme on small rimmed baking sheet. Sprinkle with salt and pepper. Bake until golden, about 25 minutes. Drizzle one tablespoon vinegar over shallots, toss to coat. Continue roasting until shallots caramelize, stirring occasionally, about 10 minutes. Remove from oven.
Bring red wine, port, brown sugar, remaining four tablespoons vinegar and granulated sugar to boil in heavy large saucepan over medium-high heat, stirring until sugar dissolves. Add cranberries; cook until berries pop, stirring occasionally, about eight minutes. Mix in parsley and shallots. Transfer to bowl. Cover and chill overnight. Serve cold or at room temperature.
This recipe can be made up to a week in advance if kept refrigerated.