Depending on browser you may not have a choice. jQuery will work with older browsers like IE7 which don't have the Nth child selector.
Ideally you should use css. The stylesheet is the best place for styles to go.
I would use css with a javascript backup for older browsers. If, for example, you want to zebra all tables try this:
tr:nth-child(2n+1), tr.odd { background:#911100; }
tr:nth-child(2n), tr.even { background:#222200; }
And in jQuery add the .odd and .even classes if the browser is old.
//You will need to check which browsers don't support n-th child. But I doubt IE will for example...
if($.browser.msie && $.browser.version < 9) {
$('tr:odd').addClass('odd');
$('tr:even').addClass('even');
}