First of all add the id
as the value parameter of the checkbox
as an input without a value is of little real use:
<table id="mytable">
<tr><th>checked</th><th>id</th></tr>
<tr><td><input id="cb1" type="checkbox" name="checker1" value="123" /></td><td>123</td></tr>
<tr><td><input id="cb1" type="checkbox" name="checker1" value="456" /></td><td>456</td></tr>
<tr><td><input id="cb1" type="checkbox" name="checker1" value="789" /></td><td>789</td></tr>
</table>
Then in jQuery, create your array:
var checkedValues = $("input:checkbox:checked", "#mytable").map(function() {
return $(this).val();
}).get();
alert(checkedValues.join(','));
Working fiddle