Better way of getting time in milliseconds in javascript?

Try Date.now().

The skipping is most likely due to garbage collection. Typically garbage collection can be avoided by reusing variables as much as possible, but I can't say specifically what methods you can use to reduce garbage collection pauses.

I know this is a pretty old thread, but to keep things up to date and more relevant, you can use the more accurate performance.now() functionality to get finer grain timing in javascript.

window.performance = window.performance || {};
performance.now = (function() {
    return performance.now       ||
        performance.mozNow    ||
        performance.msNow     ||
        performance.oNow      ||
        performance.webkitNow ||            
        Date.now  /*none found - fallback to browser default */
})();

As far that I know you only can get time with Date.

Date.now is the solution but is not available everywhere : https://developer.mozilla.org/en/JavaScript/Reference/Global_Objects/Date/now.

var currentTime = +new Date();

This gives you the current time in milliseconds.

For your jumps. If you compute interpolations correctly according to the delta frame time and you don't have some rounding number error, I bet for the garbage collector (GC).

If there is a lot of created temporary object in your loop, garbage collection has to lock the thread to make some cleanup and memory re-organization.

With Chrome you can see how much time the GC is spending in the Timeline panel.

EDIT: Since my answer, Date.now() should be considered as the best option as it is supported everywhere and on IE >= 9.