You can use .delay() before an animation, like this:
$("#myElem").show().delay(5000).fadeOut();
If it's not an animation, use setTimeout() directly, like this:
$("#myElem").show();
setTimeout(function() { $("#myElem").hide(); }, 5000);
You do the second because .hide() wouldn't normally be on the animation (fx) queue without a duration, it's just an instant effect.
Or, another option is to use .delay() and .queue() yourself, like this:
$("#myElem").show().delay(5000).queue(function(n) {
$(this).hide(); n();
});