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First, PB ist about whole, natural foods. Atkins is just about carbohydrate restriction and weight loss, whereas paleo/primal eating is about improving overall help, building strong, functional bodies and leading a life according to natural rhythms and our genetical heritage.
Although not as explicit as PB, Atkins is indeed about "whole, natural foods." (I'm talking about the Atkins plan as Dr. Atkins prescribed it in his 2002 book, not the bars/shakes/desserts pushed by Atkins Nutritionals, Inc., post-Dr. Atkins' death). Atkins is not a butter/bacon/sausage diet. The on-going weight loss phase of Atkins, the pre-maintenance phase, and the maintenance phase require you to eat "whole, natural foods" such as fruits, veggies, nuts/seeds, etc. (Atkins is much more than the two-week-ish "induction" phase, designed primarily to induce ketosis and break cravings.) I've done PB and Atkins, and except for carb counting (which I don't do on PB), there aren't many terribly different dietary differences in my daily food choices.
I would also agree with TheNomad's second point, that Atkins is more akin to a weight-loss plan whereas PB is more holistic, as Katt puts it.
I agree with Brian, having done Atkins some 10 years ago (lost 60 lbs at the time, unfortunately returned to high carb eating and put it all beck). Whole, natural foods are recommended on that diet/way of eating.
The main difference, from my point of view, is that Atkins allows grains, dairy and sweeteners. That made it more difficult for me, as those things kept giving me cravings for sweet and starchy foods. Now that I've cut out all grains and dairy (and sweeteners, but I've done that some time ago) I find I have absolutely no cravings.
Having done Atkins and changed to PB, I feel the biggest difference is the level of restrictions. On Atkins, I was always worried about which vegetables I can eat on this phase or that one. With PB there is an ideal I strive for always making choices that take me closer to the ideal.
PB feels much more natural to me. I am not desperately checking charts and adding to make sure I am consuming less that the alloted carbs. Instead I eat healthy whole foods, trusting that nature is doing the counting for me.