Theming tables

Not sure about the theme_table function, but if you're using views to build your tables you can add css classes easily enough.

I know this thread is a year old, but since I went looking for the same answer and didn't find it here, I went into the source in includes/theme.inc. The answer is in the comments for the theme_table function (which I imagine you found by now, but I put here for others to find):

* @param $rows
* An array of table rows. Every row is an array of cells, or an associative
* array with the following keys:
* - "data": an array of cells
* - Any HTML attributes, such as "class", to apply to the table row.
*
* Each cell can be either a string or an associative array with the following keys:
* - "data": The string to display in the table cell.
* - "header": Indicates this cell is a header.
* - Any HTML attributes, such as "colspan", to apply to the table cell.

So, this should give you the col1, col2, etc attributes you are looking for (plus I also gave each row a distinct class):

 $attrs = array('class' => 'my-table-class');  // optional table level attributes        
  $headers = array('col one', 'col two', 'col three');
  $rows = array();
  $data = array
    (array(1,2,3),
     array(4,5,6),
     array(7,8,9));

  $i = 1;
  foreach ($data as $cols) {
    $rows[] = array('data' => array
                    (array('data' => $cols[0], 'class'=> 'col1'),
                     array('data' => $cols[1], 'class'=> 'col2'),
                     array('data' => $cols[2], 'class'=> 'col3')),
                    'class' => "row$i");
    $i++;
  }
  $tbl = theme('table', $headers, $rows, $attrs);

The code above produces this HTML:

<table class="my-table-class sticky-enabled">
 <thead><tr><th>col one</th><th>col two</th><th>col three</th> </tr></thead>
<tbody>
 <tr class="row1 odd"><td class="col1">1</td><td class="col2">2</td><td class="col3">3</td> </tr>
 <tr class="row2 even"><td class="col1">4</td><td class="col2">5</td><td class="col3">6</td> </tr>
 <tr class="row3 odd"><td class="col1">7</td><td class="col2">8</td><td class="col3">9</td> </tr>
</tbody>
</table>