Well, look, I'm going to give you the Poor Mans Atkins answer. I am not a dietition or Doctor so take it as you like.
As I understand it, the healthiest foods and things out there are those items with very few ingrediants in them. The more natural the better. I mean, if it grew in the dirt, it probaly better that something a machine made in a tube. Our bodies are designed to handle the fresh and wholesome ingrediants. That being said, if you look at an atkins bars ingrediants you will find the following:
Taken from Atkins Peanut Butter Bar
Now I eat Atkins bars. I think they work great as a substitute and do wonderful at getting me out of tempting situations, but I can't say they are as wholesome as an apple or a carrot. For some of us, it may be better to eat the natural foods so we stay away from these processed items all together. For others, these bars may be the lesser of a far greater evil which comes from other junk food on the market. It's really your personal call.
I can;t say that Atkins bars are very healthy, but personally I can say that in a way they helped me get control of my weight and save my life.