Place colander in a medium bowl. Line colander with 4 layers of cheesecloth, allowing cheesecloth to extend over outside edges. Spoon yogurt into colander. Cover loosely with plastic wrap; refrigerate 12 hours. Spoon yogurt cheese into a bowl; discard liquid. Cover and refrigerate.
Combine the plums, 3 tablespoons honey, cinnamon, and nutmeg in a large saucepan; bring to a boil over medium-high heat. Reduce heat, and simmer 45 minutes, stirring occasionally. Remove from heat. Cool 5 minutes; stir in butter. Cool completely.
Preheat oven to 400°.
Working with 1 wonton wrapper at a time (cover remaining wrappers with a damp towel to prevent drying), spoon about 1 tablespoon plum mixture into center of wrapper. Moisten edges of dough with water, and top with another wrapper. Press 4 edges together to seal. Place ravioli on a large baking sheet coated with cooking spray (cover ravioli with a damp towel to prevent drying). Repeat procedure with remaining wrappers and plum mixture. Bake at 400° 14 minutes or until golden.
Combine 1/2 cup honey, rind, and thyme in a small saucepan over low heat. Cook 20 minutes (do not boil). Place 3 raviolis on each of 3 plates. Drizzle 2 teaspoons honey mixture over each serving; top with about 1 tablespoon yogurt cheese.