First answer

__proto__ is the actual object that is used in the lookup chain to resolve methods, etc. prototype is the object that is used to build __proto__ when you create an object with new:

( new Foo ).__proto__ === Foo.prototype;
( new Foo ).prototype === undefined;

Second answer

Prototype property is created when a function is declared.

For instance:

 function Person(dob){
    this.dob = dob
 }; 

Person.prototype property is created internally once you declare above function.
Many properties can be added to the Person.prototype which are shared by Person instances created using new Person().

// adds a new method age to the Person.prototype Object.
Person.prototype.age = function(){return date-dob}; 

It is worth noting that Person.prototype is an Object literal by default (it can be changed as required).

Every instance created using new Person() has a __proto__ property which points to the Person.prototype. This is the chain that is used to traverse to find a property of a particular object.

var person1 = new Person(somedate);
var person2 = new Person(somedate);

creates 2 instances of Person, these 2 objects can call age property of Person.prototype as person1.age, person2.age.

In the above picture you can see that Foo is a Function Object and therefore it has a __proto__ link to the Function.prototype which in turn is an instance of Object and has a __proto__ link to Object.prototype. The proto link ends here with __proto__ in the Object.prototype pointing to null.

Any object can have access to all the properties in its proto chain as linked by __proto__ , thus forming the basis for prototypal inheritance.

__proto__ is not a standard way of accessing the prototype chain, the standard but similar approach is to use Object.getPrototypeOf(obj).

Below code for instanceof operator gives a better understanding:

object instanceof Class operator returns true when an object is an instance of a Class, more specifically if Class.prototype is found in the proto chain of that object then the object is an instance of that Class.

function instanceOf(Func){
var obj = this;
while(obj !== null){
    if(Object.getPrototypeOf(obj) === Func.prototype)
        return true;
    obj = Object.getPrototypeOf(obj);
}
return false;
}

The above method can be called as : instanceOf.call(object,Class) which return true if object is instance of Class.

Third answer

A nice way to think of it is…

prototype is used by constructor() functions. It should’ve really been called something like, "prototypeToInstall", since that’s what it is.

and __proto__ is that “installed prototype” on an object (that was created/installed upon the object from said constructor() function)