You could use {$smarty.now} in the subject line as a unique numeric identifier (unix timestamp).
Edit skin/common_files/mail/help_contactus_subj.tpl
Eg.
Code:
{config_load file="$skin_config"}{$config.Company.company_name}: {$lng.eml_contact_us_subj} | {$smarty.now} | {$smarty.now|date_format:$config.Appearance.date_format} | {$smarty.now|date_format:$config.Appearance.time_format} | {$contact.firstname} {$contact.lastname} | {$contact.email} | {$contact.subject}
And/or add the necessary code to skin/reboot/mail/html/help_contactus.tpl