Parse.com query executing after the fact

This should give you something to go on, im not sure if it will work but it should show you the concept.

What you need to do is create an array of promises as it looks like your performing a query for each item in an array, and because the queries take some time your response is sent before the queries are complete. You then evaluate the array of promises and send your response back only when they are resolved.

I would suggest you split your logic into a few more functions as it's a little hard to follow.

Take a look at the parallel promises section

function processNavigation(navigation) {
    var nav = [];
    var promises = []

        _.each(navigation, function(navItems) {
            var navProperties = {
                name: navItems.get("Name"),
                longName: navItems.get("LongName"),
                icon: navItems.get("Icon"),
                url: navItems.get("Url"),
                module: navItems.get("Module"),
                runScript: navItems.get("RunScript"),
                sortOrder: navItems.get("SortOrder")
            };

            switch (navItems.get("Module")) {
                case "lists":
                    promises.push((function(navProperties){
                        var listsQuery = new Parse.Query("ListItems"); // This should return back! But it's async? Needs promise?
                        listsQuery.ascending("SortOrder");
                        listsQuery.find().then(
                            function(results) {
                                var list = [];
                                _.each(results, function(listItems) {
                                    var listProperties = {
                                        name: listItems.get("Name"),
                                        subName: listItems.get("Subname"),
                                        sortOrder: listItems.get("SortOrder")
                                    };
                                });
                                list.push(listProperties);
                                navProperties["source"] = list;
                                promise.resolve();
                            },
                            function() {
                                promise.reject();
                                res.send('error');
                            }
                        );
                    })(navProperties))

                    break;

                default:
                    navProperties["source"] = null;
                    break;
            }

            nav.push(navProperties);
        });


        Parse.Promise.when(promises).then(function(){                               
            res.send(nav);
        })

    }