Heat olive oil in a large nonstick skillet over medium-high heat. Add onion; saute 3 minutes. Add thyme and garlic; saute 1 minute. Stir in rice; saute 1 minute. Stir in wine; cook 1 minute or until liquid is nearly absorbed, stirring constantly. Add water and salt; bring to a boil. Cover, reduce heat, and simmer 18 minutes. Remove from heat. Stir in cheese, butter, truffle oil, and pepper. Cool.
Preheat oven to 375°.
Place 1 phyllo sheet on a large cutting board or work surface (cover remaining dough to keep from drying); lightly coat sheet with cooking spray. Repeat layers with remaining phyllo and cooking spray, ending with phyllo. Gently press phyllo layers together. Lightly coat top phyllo sheet with cooking spray. Cut phyllo layers into 24 (1 1/2-inch) squares using a sharp knife or pizza cutter.
Carefully place 1 layered square in each of 24 miniature muffin cups coated with cooking spray; gently press squares into pan to form cups. Bake at 375° for 5 minutes or until crisp. Remove phyllo cups from pan. Fill each cup with 1 tablespoon risotto. Sprinkle cups evenly with parsley.