First, you have to understand that timers in javascript are not guaranteed to be called on time so therefore you cannot be perfectly synced at all times - javascript just isn't a real-time language like that. It is single threaded so a timer event has to wait for other javascript that might be executing at the time to finish before a timer can be executed. So, you must have a design that still does as best as possible even if the timer is delayed (called later than it's supposed to be).
If you wanted to try to stay as close to aligned and do the fewest screen updates and be the most friendly to mobile battery life, I'd suggest this self-aligning code which realigns itself on each tick based on the time remaining until the next minute change:
function runClock() {
var now = new Date();
var timeToNextTick = (60 - now.getSeconds()) * 1000 - now.getMilliseconds();
setTimeout(function() {
update();
runClock();
}, timeToNextTick);
}
// display the initial clock
update();
// start the running clock display that will update right on the minute change
runClock();
This has the advantage that it only calls the update once on the next minute boundary.
Working demo: http://jsfiddle.net/jfriend00/u7Hc5/