I may be misunderstanding the question, but wouldn't all the emails on your server be considered new if they haven't been downloaded by a mail client? Normally a mail program will download and save messages on your machine, or delete them off the server entirely, so the next it checks the server, any messages there are new. So if you're not downloading or deleting those messages, you'll have to save the date and time of when you check the server in a file somewhere. That way, the _next_ time you look for mail, any messages that are newer than the date in the file can be marked as new.
"We're experiencing some Godzilla-related turbulence..."