Edit in JSFiddle

$(document).ready(function () {
    var colors = new Array("red", "yellow", "blue");
    var size = 3;
    var startPos = -1;
    var speed = 20000;
    var cantidad = 500;

    setInterval(function () {
        var color = colors[random(0, 3)];
        var w = window.innerWidth;
        var h = window.innerHeight;

        var e = document.createElement("span");
        $(e).css("display", "inline-block");
        $(e).css("width", size + "px");
        $(e).css("height", size + "px");
        $(e).css("background", color);
        $(e).css("position", "fixed");
        $(e).css("top", startPos + "px");
        $(e).css("left", random(0, w) + "px");
        $(e).css("z-index", "1000");
        $(e).animate({ top: h + "px" }, speed, "linear", function () {
            this.remove();
        });
        $("html").append(e);
    }, cantidad);
});
function random(min, max) {
    return Math.floor((Math.random() * max) + min);
}