Heat oven to 400° F.
In a roasting pan, toss the fennel, onion, garlic, tomatoes, thyme, 1/2 teaspoon of the salt, 1/4 teaspoon of the pepper, and the oil. Spread evenly and roast for 20 minutes.
Move the vegetables to side of pan, add the salmon, then redistribute the vegetables around the salmon. Squeeze the lemon halves over the salmon. Sprinkle the salmon with the remaining salt and pepper. Return to oven and roast until the salmon is the same color throughout and flakes easily, 10 to 12 minutes. Serve immediately, with the rice, if desired.
Tip: When estimating how long to cook fish, allow about 10 minutes for each inch of thickness.