I want this ability too. We use to use Fogbugz and we would just put the ticket ID number in the subject line. It would go directly to the ticket. I've tested with zendesk using the modified email address support+id{ticket.id}@domain.zendesk.com and have had mixed results. It worked once but on newly created ticket it wouldn't work. Plus it's more of pain and less user friendly to have to modify the email.

Something like

Subject: FWD: blah blah #4442

Then zendesk would see # and read number after it, then forward it to the existing ticket. Then this feature could be enabled or disabled in the administrator settings if they didn't like it.