I think it depends what you are looking for. In absolute terms, I would say that Concord is the more desirable town. Same answer if you are looking for a home based on quality of education.
But, if your kids are not ready for high school, you can find areas of the other two that have great elementary schools, and you will pay significantly less in taxes. Both Natick and Waltham have strong business communities that shell out a large portion of the city/town budgets. Also, depending where in Waltham you are talking about, the commute to downtown Boston is a little easier than Concord, as you can just jump on the Mass Pike rather than go Rt. 2 to Sturrow Drive. Also, I believe you can get the same size house in Waltham or Natick as you could in Concord for significantly less.
But, as I said, in absolute terms, Concord is considered the more desirable community.
I think that is a popular misperception of Waltham. While Waltham does have Moody Street, and is close to Watertown and Cambridge, it also have some very popular residential neighborhoods. Also, all Waltham elementary schools have been rebuilt in the last few years, with the last one, the Fitzgerald, scheduled to open next year. As they go through this process, the schools neighborhoods and schools have received very good reviewes (top ten elementary schools by Boston Magazine, and top ten streets by Boston Magazine). I looked at Waltham at one point, and was surprised at the amount of people from Newton and Belmont that were looking for houses in Waltham to start a family. Take a look at the Warrendale neighborhood on the Belmont border, and the neighborhoods near Bentley off of Forest Street.