My quick example:

<select multiple id="select">
    <option value="1">1</option>
    <option value="2" class="toselect">2</option>
    <option value="3">3</option>
    <option value="4" class="toselect">4</option>
    <option value="5">5</option>
</select>
<script type="text/javascript">
    var select = document.getElementById("select");
    var select_options = select.getElementsByClassName("toselect");
    for (var i = 0; typeof(select_options) != "undefined"; i++) {
        select_options[i].selected = true;
    }
</script>

Here, I'm using class names to designate which options needs to be selected. You can use whatever you want.

Something like this:

var selectBox = document.getElementById('selectbox');

selectBox.children[1].selected = true;

​ Complete example: jsFiddle