In medium bowl, combine the peppers, red-pepper flakes, and thyme. Add the oil and vinegar, and toss to coat. Season with salt and pepper. Cover with plastic wrap, and let sit, at room temperature, for 1 hour.
Preheat oven to 350 degrees. Spread peppers on a baking sheet, and bake until tender but not mushy, about 30 minutes, stirring every 10 minutes. Store refrigerated, in an airtight container, for up to 5 days.