If you want to have the columns end up the same height, which is to say, pad out the divs that are smaller then their neighbors you could change the css to something like this:
.box {background:#20abff; color:#fff; width: 5px; margin: 5px;}
.left {float:left;}
.right {float:left;}
.container {width:200px;}
Another thing you could do is to make pseudo tables with divs.
.Table_Wrapper { width: 400px; }
.Table_Row { width: 98%; padding: 1%;float: left; }
<div class="Table_Wrapper">
<div class="Table_Row">
<div class="box left" style="height:60px;">1</div>
<div class="box right" style="height:80px;">2</div>
</div>
<div class="Table_Row">
<div class="box left" style="height:60px;">3</div>
<div class="box right" style="height:60px;">4</div>
</div>
<div class="Table_Row">
<div class="box left" style="height:60px;">5</div>
<div class="box right" style="height:60px;">6</div>
</div>
</div>
JSFiddle