AMDWTF: So you want to AMD...

arena.js

define( [ 'jquery', 'mods/crazydot' ], function( $, CrazyDot ){
    var dots = [];

    var setup = function( cfg ){
        while ( dots.length < cfg.count ){
            dots.push( new CrazyDot( cfg.speed, 'body' ).move() );
        }
    };

    var stopGame = function(){
        eachDot(function( dot ){
            dot.stop();
        });
    };

    var startGame = function(){
        eachDot(function( dot ){
            dot.start();
        });
    };

    var setSpeed = function( spd ){
        eachDot(function( dot ){
            dot.speed = spd;
        });
    };

    var eachDot = function( callback, ctx ){
        for ( var i = 0, l = dots.length; i < l; i += 1 ){
            callback.call( ctx, dots[ i ], i );
        }
    };

    // public api /////////////////////////////////////////////////////////////
    return {
        setup : setup,
        stopGame : stopGame,
        startGame : startGame,
        setSpeed : setSpeed
    };
});

configs.js

define({
    speed: 1000,
    count: 10
});

crazydot.js

define( [ 'jquery' ], function( $ ){
    var dotCount = 0;

    var CrazyDot = function ( speed, target ){
            var self = this;

            dotCount += 1;

            this.speed = speed;
            this.$dot = $('<div class="dot">' + dotCount + '</div>').appendTo( target );
            this.width = this.$dot.outerWidth(true);
            this.height = this.$dot.outerHeight(true);

            //click handler
            this.$dot.click(function() {
                if (!self.isPaused){
                    self.stop();
                } else {
                    self.start();
                }
            });
        };

    CrazyDot.prototype = {
        isPaused : false,
        start : function start(){
            this.isPaused = false;
            this.$dot.removeClass('is-paused');
            this.move();
            return this;
        },
        stop : function(){
            this.isPaused = true;
            this.$dot.addClass('is-paused');
            return this;
        },
        move : function move(){
            var maxX = $(document).width(),
                maxY = $(document).height(),
                self = this;

            this.$dot.animate({
                    top: Math.floor(Math.random() * ( (maxY - this.height) - 0 + 1)) + 0,
                    left: Math.floor(Math.random() * ( (maxX - this.width) - 0 + 1)) + 0
                },
                this.speed * (Math.random() + .25),
                function(){
                    if (!self.isPaused) {
                        self.move();
                    }
                });
            return this;
        }
    };

    // public api /////////////////////////////////////////////////////////////
    return CrazyDot;
});

main.js

require.config({
    paths : {
        'jquery' : 'http://code.jquery.com/jquery-latest'
    }
});
require( [ 'jquery', 'mods/arena', 'mods/configs' ], function( $, arena, configs ){
    $( document ).ready(function(){
        arena.setup( configs );

        $('#js-controls').on( 'click', '.control', function( e ){
            e.preventDefault();
            switch ( e.currentTarget.hash.replace( '#', '' ) ){
                case 'stop':
                    arena.stopGame();
                    break;
                case 'start':
                    arena.startGame();
                    break;
                case 'halfspeed':
                    arena.setSpeed( configs.speed * 2 );
                    break;
                case 'fullspeed':
                    arena.setSpeed( configs.speed );
                    break;
                case 'dblspeed':
                    arena.setSpeed( configs.speed / 2 );
                    break;
            }
        });
    });
});