javascript: pause setTimeout();

You could wrap window.setTimeout like this, which I think is similar to what you were suggesting in the question:

var Timer = function(callback, delay) {
    var timerId, start, remaining = delay;

    this.pause = function() {
        window.clearTimeout(timerId);
        timerId = null;
        remaining -= Date.now() - start;
    };

    this.resume = function() {
        if (timerId) {
            return;
        }

        start = Date.now();
        timerId = window.setTimeout(callback, remaining);
    };

    this.resume();
};

var timer = new Timer(function() {
    alert("Done!");
}, 1000);

timer.pause();
// Do some stuff...
timer.resume();