The imagined savior
One obvious symbol is the titular Nutcracker. In the context of the war against the mice, the Nutcracker is a savior character, because he will save the toy people from their impending doom. This is especially significant given that these characters belong to a religious community and they're celebrating Christmas. In the context of Marie's imaginary world, the savior character represents hope that the future can bring something good, in spite of Marie's fear of time.
The clockwork world
When the children pester their godfather enough, they finally figure out what it is that he made for them—a little clockwork world with puppets that come out in time (like a cuckoo clock). They are fascinated by the world, but because the world is timed, it is predictable to them, and before very long, the kids are bored of the clock. They want something exciting and unpredictable, so Marie begins to invent an imaginary story about the toy world. The clock world represents the children's unlikely preference for unpredictability. It is as if they understand that they are supposed to be entertaining themselves. By the end of the book, we know why—they are using their imaginations to deal with painful emotions.
The mice as a symbol for decay
Mice in the estate indicates the passage of time, because older houses tend to become infested with mice. Mice are also animals, which means they represent nature, because they are literally compelled by their nature. They are violent and they bring chaos and pain to the toy community. In other words, they make things worse over time, which makes them into a force of decay.
Pirlipat's curse
In Marie's imagination, she invents a beautiful princess. She imagines a beautiful girl, more beautiful than any other person in any universe. This makes Pirlipat archetypal because she is the "most" beautiful girl in the world, so she represents the fullness of Marie's desire to be beautiful. So when Pirlipat is cursed with a hideous face, Pirlipat comes to represent Marie's fear of being ugly.
The Christmas motif
This is a thoroughly "Christmas" story. It starts on Christmas eve, for starters. It concerns the basic theme of a young girl coming to terms with the horror and pain of life (by exploring imaginary stories in midnight trances). That might not seem very Christmas-like, but it absolutely is. In this story, the Christmas spirit is the opposite of time's decay. Christmas represents hope and new life. It is important to consider that perhaps Marie is mourning the loss of her parents, which is something that would make Christmas very lonely and painful. It is not unusual for Christmas to represent such painful things for this specific reason.
