Place squash on a microwave-safe plate, microwave on high for 3-4 minutes. Cut in half; remove seeds and strings. Cut a thin slice from bottom of squash with a sharp knife to allow it to sit flat. Place squash, cut side down on in a microwave-safe dish. Cover and microwave for 4-1/2 minutes.
Meanwhile, combine the crackers, butter, brown sugar and nutmeg. Turn squash over; fill with cracker mixture. Microwave for 1-2 minutes or until squash is tender.