I think you're saying that you have a third-party program that needs to poll a POP3 or IMAP mailbox for messages and you want to know if you can "serve" the POP3 or IMAP protocol from Exchange and have the third-party program poll an Exchange mailbox with POP3 or IMAP to receive messages. I'm going to proceed with my answer on that basis.
You can absolutely use the POP3 or IMAP server in Exchange 2003 to allow a third-party program to access an Exchange mailbox. The POP3 and IMAP servers in Exchange access the same mailbox storage database that clients running Outlook and Outlook Web Access use.
The high-level steps you need to take would be:
Create a mailbox enabled Active Directory user account to store the third-party program's messages. Set the password and alias during account creation with the values you desire. (To make life easiest, you should configure the account's username and Exchange alias to be the same.)
Start the POP3 or IMAP service on the Exchange Server computer.
Configure the third party program with the name or IP address of the Exchange Server computer as its POP3 or IMAP server. Configure it with the username and password of the AD account you created for the third-party software.
You can logon to the mailbox for the third-party software using Outlook Web Access or Outlook to verify that messages are being received. If the third-party software complains about not being able to access its mailbox I'd use a sniffer to examine the traffic to determine why the access is failing.
If you don't set the username and Exchange alias to be identical when creating the user account for the third-party software you will need to specify the username in the format of DOMAIN\username\alias when you enter the POP3 / IMAP username into the third-party software.