How to force Sequential Javascript Execution?

Well, setTimeout, per its definition, will not hold up the thread. This is desirable, because if it did, it’d freeze the entire UI for the time it was waiting. if you really need to use setTimeout, then you should be using callback functions:

function myfunction() {
    longfunctionfirst(shortfunctionsecond);
}

function longfunctionfirst(callback) {
    setTimeout(function() {
        alert('first function finished');
        if(typeof callback == 'function')
            callback();
    }, 3000);
};

function shortfunctionsecond() {
    setTimeout('alert("second function finished");', 200);
};

If you are not using setTimeout, but are just having functions that execute for very long, and were using setTimeout to simulate that, then your functions would actually be synchronous, and you would not have this problem at all. It should be noted, though, that AJAX requests are asynchronous, and will, just as setTimeout, not hold up the UI thread until it has finished. With AJAX, as with setTimeout, you’ll have to work with callbacks.