Cut the onions in half vertically and then into 1/4 inch thick slices (not paper thin or they’ll get mushy). Place on a baking sheet and toss with olive oil, thyme, salt, and pepper and 1/4 cup balsamic vinegar.
Bake on the middle rack for 30 minutes, turning once or twice, until the onions are soft and lightly caramelized. Remove from the oven, and while they’re still hot, pour over 2 more tablespoons balsamic vinegar. Toss to coat. Can be served warm or at room temperature.