Cook spinach according to package directions. Drain and set aside.
Remove stems from tomatoes, and cut a 1/4-inch slice from the top of each. Scoop out pulp, leaving shells intact. Reserve pulp for use in another recipe. Invert tomato shells on paper towels to drain; set aside.
Sauté onion in butter in a medium saucepan over low heat until tender. Add spinach, breadcrumbs, eggs, salt, and thyme; stir well. Spoon mixture into prepared tomato shells. Sprinkle cheese over top of tomatoes. Place tomatoes in two lightly greased baking dishes. Bake at 350° for 20 minutes or until browned. Serve immediately.