Nuts are a very similar situation to fruit. Good in small amounts, but problematic in large doses.
The big gotcha with nuts is omega-6 fat. Omega-6 fat, along with omega-3 fat are essential fats - essential because they can't be produced by your body. If you didn't eat any omega-6 fat you would eventually die.
That does not mean you should eat as much as possible? No. Moderation, people!
The deal here is that omega-3 fat is anti-inflammatory and omega-6 fat is pro-inflammatory. Both functions are critical to life. Inflammation, while it sounds bad, is a necessary function in your body. This is how you fight infection. This is how you recover from injuries.
But a little inflammation goes a long way. As it turns out, Americans get way more omega-6 fat compared to omega-3 fat. Our (not so) healthy friend, vegetable oil is very high in omega-6 fat. Corn oil is the worst offender at over 90% omega-6 fat. A meal cooked with vegetable oil is way, way, way, more than a person needs.
According to the Paleo diet gurus a good ratio of omega-6 to omega-3 fat is 1:1 to 2:1. A typical American is eating 10:1 to 20:1. This combination of high amounts of pro-inflammatory fat and low anti-inflammatory fat means the body is always biased toward inflammation. This is a very bad thing. Inflammation is meant to be a temporary thing. By eating like this your body is basically in a state of martial law all the time.
So, nuts are great by themselves and in moderation. Combined with an already high omega-6 problem they are making the problem worse.
Of course the correct thing to do is to not eat any vegetable or nut oils. Then you can enjoy your whole nuts at one serving (a single handful) a day.
Oh yeah, don't eat them raw. Cooking breaks down their natural toxins.