Overriding/Extending the Magento core javascript files

See this from prototype manual http://prototypejs.org/doc/latest/language/Function/prototype/wrap/ you can wrap whatever object method and even call "parent" if needed and here's a pseudo sample:

//where Product.Config is the object/class you need to "override"
Product.Config.prototype.getOptionLabel  = Product.Config.prototype.getOptionLabel.wrap(function(parentMethod){
    //replace the original method here with your own stuff
    //or call parentMethod(); if conditions don't match
});

Just to add to @anton-s's absolutely correct answer, you can also do "full" class rewrites:

// Create the original class
var ClassA = Class.create();
ClassA.prototype = {
    initialize: function(config) {
        this.config = config;
    },
    test: function(msg) {
        console.log('Hi from class A with message ' + msg);
    }
};

// Create new class extending the original class
var ClassB = Class.create(ClassA, {
    // $super is a reference to the original method
    test: function($super, msg) {
        console.log('Hi from class B');
        console.log('this.config is accessible in class B: ' + this.config);
        $super(msg + ' ...')
    }
});


// To make the extend an override, you can do this:
ClassA = ClassB;
// ClassA now is ClassB overriding the original ClassA
var a = new ClassA('some config data');
a.test('Call A 1');

Since all this only works on prototype classes, not on already instantiated objects, I'll also throw in this hack, which is pretty much what wrap() does, too:

// Overriding a method of an already instantiated object
// There are many ways to do this more elegantly thanks to the amazing JS scoping magic
a.origTest = a.test;
a.test = function(msg) {
    console.log('Hi from the patched method');
    this.origTest(msg);
}
a.test('Call A 2');

Keep in mind though that the wrap() method is nicer, and can also be used on on class definitions or on concrete instances.

// Wrap method of concrete instance
spConfig.getOptionLabel = spConfig.getOptionLabel.wrap(function(parentMethod, option, price) {
    return parentMethod(option, price);
});

// Wrap method of class declaration
Product.Config.prototype.getOptionLabel = Product.Config.prototype.getOptionLabel.wrap(function(parentMethod, option, price) {
    return parentMethod(option, price);
});