MultiPageApp.js

// app reflects server-side pages
var App = {
	Store: {
		Index: {},
		Product: {},
		Category: {},
		ContentPage: {}
	}
};

// A class for each page
App.Store.Index = new Class({ /* class logic goes here */ });
App.Store.Product = new Class({ /* class logic goes here */ });
App.Store.Category = new Class({ /* class logic goes here */ });
App.Store.ContentPage = new Class({ /* class logic goes here */ });

SampleController.js

var App = new Class({
	
	Implements: [Options,Events], 

		options: {
			// options, sometimes put selectors for 'nodes' up here
		},

	initialize: function(options){
		// elements on the page
		this.nodes = {
			nav:        $('main-nav'),
			slideshows: $$('.slideshow'),
			sidebar:    $('sidebar')
		};

		// bound events so I can remove them later (and keep things more organized)
		this.bound = {
			navClick:     this.navClick.bind(this),
			showComplete: this.showComplete.bind(this),
			hideSidebar:  this.hideSidebar.bind(this)
		};
		
		// properties
		this.property = 0;
		
		// stuff to run up front
		this.build().setup().attach();
		
	},
	
	build: function(){
		// create new elements with javascript
		return this;
	},
	
	setup: function(){
		// instantiate other objects, and do any other random stuff
		this.nodes.slideshows.each(function(element){
			this.slideshows.push(new Slideshow(element,{ duration: 3000, transition: 'crossFade' }));
		}, this);
		return this;
	},
	
	attach: function(){
		// element events
		this.nodes.sidebar.addEvent('click', this.bound.hideSidebar);
		this.nodes.nav.each(function(element){
			element.addEvent('click', this.bound.navClick);
		}, this);
		
		// instance events
		this.slideshows.each(function(slideshow){
			slideshow.addEvent('showComplete', this.bound.showComplete);
		}, this);
		
		return this;
	},
	
	// event handlers
	navClick: function(){
		// logic when the nav is clicked
		return this;
	},
	
	showComplete: function(){
		// logic to do whenever a slideshow is complete
		return this;
	},
	
	sidebarHide: function(){
		this.nodes.sidebar.hide();
		return this;
	},
	
	// any other helper methods
	
	tellTheTruth: function(){
		return true;
	}

});