JavaScript doesn't have namespaces. What you're calling a namespace is just an object. It's fairly common to use objects to stand in for namespaces.
Your code:
var namespace = {};
namespace.something.nested.namespacing();
...creates an object and a variable that refers to that object called namespace. Then you add properties to that object (it looks like you've added a property, something, which is also an object, which has a property, nested, which is also an object, which has a property called namespacing which refers to a function).
Your code:
something.prototype.method();
...is also using an object. The above would actually be a really unusual thing to do, you're calling a function (method) by directly referring to the prototype property of what I assume is a function (something). That's not normally what you would do. Normally you'd create an object via the function:
var s = new something();
...and then use the prototype that got assigned to s implicitly:
s.method();
The prototype property on functions can be confusing to people new to JavaScript. It's just a normal property like any other property, which is on function instances. The only thing that makes it special is the new operator: When you call a function via new:
var s = new something();
...the JavaScript engine creates a new, blank, object, then sets its underlying prototype (sometimes called __proto__ but that's not in the spec [yet]) using something.prototype, like this:
// pseudo-code for `var s = new something()`
var tmp = {}; // New, blank object
tmp.__proto__ = something.prototype; // Assign a prototype to the new object
something.call(tmp); // Call `something` with `this` referring to `tmp`
s = tmp; // Assign the result to `s`
(There's a detail I left out in the above to avoid confusing matters, to do with the special case where something has an explicit return statement in it that returns an object reference.)
prototype".[[Prototype]], then that object's[[Prototype]]and so on. The object path in the accessing expression is irrelevant to how property lookup proceeds.