I'm not a native speaker, but I will give you my view.

In copulative sentences, that is, in sentences where the main verb is "be", subject and subject complement (of a nominal nature) are usually interchangeable:

1.a. Mary is my best friend.

1.b. My best friend is Mary.

In your first sentence, the main verb is "go", so there is no doubt that "she" is the subject and there will be no problem placing it before the auxiliary in a short answer:

- Who is going to the game tonight?
- Mary (is).

Your second and third sentences are copulative and have "be" as the main verb. "what" and "who" may then ask for the subject or for the subject complement. If the information requested is the subject, then the subject + auxiliary answer will sound fine, but if the information requested is the subject complement, it will sound odd.

Of these two pairs of sentences, we can easily tell that the one that sounds natural is that which introduces new information by means of the subject complement:

2.a. Football is the most popular sport in America.

2.b. The most popular sport in America is football. 

3.a. The name of this book is *Catcher in the Rye*.

3.b. *Catcher in the Rye* is the name of this book.

2.a. and 2.b. are equally natural. Instead, 3.a. sounds more natural than 3.b., and that is because "the name of this book" is a better candidate for subject than "Catcher in the Rye". Then, when we ask:

- What is the name of this book?

"what" is asking for the subject complement. A more natural reply will then be:

- It (The name of this book)'s *Catcher in the Rye*.