<div id="timer">
<div id="hours"></div>
<div id="minutes"></div>
<div id="seconds"></div>
<div id="names"><span>Часы</span><span>Минуты</span><span style="margin-left:-1px;">Секунды</span></div>
</div>

#hours, #minutes, #seconds {
background: -webkit-linear-gradient(top,#404040,#202020);
background: -moz-linear-gradient(top,#404040,#202020);
background: -o-linear-gradient(top,#404040,#202020);
background: -ms-linear-gradient(top,#404040,#202020);
box-shadow: 0 1px 5px #303030,inset 0 1px 0 #3d3d3d;
padding-top: 9px;
font: 16px arial;
color: white;
float: left;
margin-right: 15px;
border-radius: 2px;
text-align: center;
width: 40px;
height: 30px;
text-shadow: 0 1px 6px black;
}
.in{
box-shadow:inset  0 1px 5px #202020 !important;
-moz-box-shadow:inset  0 1px 5px #202020 !important;
-o-box-shadow:inset  0 1px 5px #202020 !important;
-ms-box-shadow:inset  0 1px 5px #202020 !important;
}
.out{
box-shadow: 0 1px 5px #303030,inset 0 1px 0 #505050;
-ms-box-shadow: 0 1px 5px #303030,inset 0 1px 0 #505050;
-moz-box-shadow: 0 1px 5px #303030,inset 0 1px 0 #505050;
-o-box-shadow: 0 1px 5px #303030,inset 0 1px 0 #505050;
}
#timer {
margin: -20px 0 0 -67px;
top: 50%;
left: 50%;
position: absolute;
width: 166px;
height: 40px;
}
#names {
color: #ccc;
font: 10px arial;
text-shadow: 0 1px 8px #000;
}
#names span {
width: 40px;
float: left;
text-align: center;
margin-right: 15px;
margin-top: 6px;
}

var message,messagetext,textd,site,sitehref;
var hour2,sec2,min2;
var set;
var whil1;
var hour1=document.getElementById("hours");
var min1=document.getElementById("minutes");
var names=document.getElementById("names");
var sec1=document.getElementById("seconds");
a=hour;
b=min;
c=sec;

function timer(){
   sec--
  if (sec==-1){
   sec=59;
   min--
  }
  if (min==-1){
   min=59;
   hour--
  }
   hour1.innerHTML=hour;
   min1.innerHTML=min;
   sec1.innerHTML=sec;
}

if (sec>59){
  sec2=Math.floor(sec/60)
  min +=sec2
  sec -= 60*sec2
}
if (min>59){
  min2=Math.floor(min/60)
  hour +=min2
  min -= 60*min2
}
hour1.innerHTML=hour;
min1.innerHTML=min;
sec1.innerHTML=sec;

if (textd==false){
  names.style.display="none";
}

function out(){
  if (sec % 2 ==0){
   sec1.className="in"
  }else{
   sec1.className="out"
  }
  if (sec ==0){
   min1.className="in"
  }else{
   min1.className="out"
  }
  if (min ==0 && sec==0){
   hour1.className="in"
  }else{
   hour1.className="out"
  }
}

function whil(){
//если время кончилось
  if(hour==0 && min==0 && sec==0){
  if (message==true){
   alert(messagetext);
  }
  if (site==true){
   window.location.href = sitehref;
  }
  if (whil1==true){
   hour=a
   min=b
   sec=c+1//ставим на 1 единицу больше
  }else if (whil1==false){
   clearInterval(set);
   clearInterval(set2);
  }
}
}

set1=setInterval(out,1000);
set2=setInterval(whil,1000);

<script>
var hour=0;
var min=69;
var sec=134;
whil1=true;
message=false;
messagetext="Message";
textd=false;
site=false;
sitehref="http://zornet.ru"
</script>