If you're talking about in a form then you can use the 'error_msg' parameter to define your own custom message, eg:
$_tmp = array(
'name' => 'profile_id',
'label' => 'profile name',
'type' => 'live_search',
'help' => 'Select the profile to reset the business settings for',
'validate' => 'not_empty',
'required' => true,
'error_msg' => 'You have selected an invalid Profile - please try again',
'target' => jrCore_get_base_url() . "/{$_post['module_url']}/search_business_profiles"
);
jrCore_form_field_create($_tmp);
if you're talking about an alert style thing then:
jrCore_alert('this is an alert message, but pretty')
You've said JAVASCRIPT so you probably dont want
jrCore_set_form_notice('error', 'invalid something');
jrCore_get_form_notice();
any of that useful, im not sure.