custom_module.js

YUI.add("myapp-base", function(Y){

    Y.MyApplication = function () {};

    // Class definition
    Y.MyApplication.prototype = {
       //...
    };

}, "3.0.0b1", {requires:["node"]});

// Submodule definition
YUI.add("myapp-submodule", function(Y){
 //...
}, "3.0.0b1", {requires:["myapp-base"]});

// Rollup definition
YUI.add("myapp", function(Y){}, "3.0.0b1", {use: ["myapp-base", "myapp-submodule"]});

Doesn't work

<script src="/my/local/yui3/build/yui/yui.js"></script>
<script src="custom_module.js"></script>
<script>

// This does not work

YUI({
    base: '/my/local/yui3/build/',
    modules:{
        myapp:{
            requires:["node"] // should be unnecessary, but fails even without this
        }
    }
}).use("myapp", function(Y) {
    // Node is NOT loaded
    debugger;
});

Works

<script src="/my/local/yui3/build/yui/yui.js"></script>
<!--script src="custom_module.js"></script-->
<script>

// This works

YUI({
    base: '/my/local/yui3/build/',
    modules:{
        myapp:{
            fullpath: 'custom_module.js',
            requires:["node"]
        }
    }
}).use("myapp", function(Y) {
    // Node is loaded
    debugger;
});