There is no big difference between those functions except the syntax:
$(\'.target\').append(\'text\');
$(\'text\').appendTo(\'.target\');
A
You said it yourself --- there's not much difference. My choice of what to use, however, normally depends on method chaining, provided you already have your elements referenced.
i.e.
var _target, _content;
_target.append(_content).addClass('foo');
// will add the foo class to _target
_content.appendTo(_target).addClass('foo');
// will add the foo class to _content