SO fiddle

Test Fiddle mainly for SO Questions

HTML

<link rel="stylesheet" href="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8/themes/dot-luv/jquery-ui.css">
<table class="altRow">
    <tr>
        <td rowspan="2">1</td>
        <td>joe</td>
        <td>1</td>
        <td>3</td>
    </tr>
    <tr>
        <td>tom</td>
        <td>2</td>
        <td>3</td>
    </tr>
    <tr>
        <td>2</td>
        <td>joe</td>
        <td>3</td>
        <td>3</td>
    </tr>
    <tr>
        <td>3</td>
        <td>joe</td>
        <td>4</td>
        <td>3</td>
    </tr>
    <tr>
        <td>4</td>
        <td>joe</td>
        <td>6</td>
        <td>3</td>
    </tr>
    <tr>
        <td rowspan="2">5</td>
        <td>joe</td>
        <td>5</td>
        <td>3</td>
    </tr>
    <tr>
        <td>tom</td>
        <td>3</td>
        <td>3</td>
    </tr>
</table>

another table

<table class="altRow">
    <tr>
        <td rowspan="2">1</td>
        <td>joe</td>
        <td>1</td>
    </tr>
    <tr>
        <td>tom</td>
        <td>2</td>
    </tr>
    <tr>
        <td>2</td>
        <td>joe</td>
        <td>3</td>
    </tr>
    <tr>
        <td>3</td>
        <td>joe</td>
        <td>4</td>
    </tr>
    <tr>
        <td>4</td>
        <td>joe</td>
        <td>6</td>
    </tr>
    <tr>
        <td rowspan="2">5</td>
        <td>joe</td>
        <td>5</td>
    </tr>
    <tr>
        <td>tom</td>
        <td>3</td>
    </tr>
</table>

CSS

td { vertical-align: top; padding: 3px; }

.alt { background-color: #DEDFDE; }

JavaScript

$("table.altRow").each(function() {
    var $this = $(this);
    var numTD = $this.find("tr:has(td[rowspan]):first td").length;
    $this.data('numTD', numTD).find("tr").filter(function() {
        var $this = $(this);
        return $this.children().length == $this.closest('table').data('numTD');
    }).filter(':even').addClass('alt');

})

$("tr.alt td[rowspan]").each(function() {
    $(this).parent().nextAll().slice(0, this.rowSpan - 1).addClass('alt');
});