I think there are positive messages in BOTH the Harry Potter books and LOTR. Both are about fighting evil, and helping others to not fall into evil ways. No, they aren't religious, but they are inspirational.
The message: Evil exists, and it is defeated by people who live the virtues of courage and loyalty. It isn't scripture, but it is a jumping off point for a message about the importance of virtue, which has an easy segue to a more explicitly religious message.
I've written before that there's a comparison to be drawn between To Kill a Mockingbird and Lord of the Rings. Atticus Finch and Samwise Gangee are heroes because of a clear moral vision and the determination to see it through. You and I can't decide to become Superman or Spiderman, but we can decide to be Atticus or Sam.
It's a Wonderful Life is inspiring for a different reason, and I can't argue with its #1 ranking. The movie came out after a decade of depression and a half-decade of war, when a lot of folks weren't where they expected to be at that point in life.
The message of the movie was that however dark things seem, however low you feel, there are angels above and friends on Earth who have your back. It's a good message for anyone at any time, but especially for its own time.