Only save to mass storage messages that are older than some amount of time. That way, the quickly retrieved ones are never committed to storage, and only the ones that hang around for longer periods of time get saved away for later retrieval.

For this to work you would probably need your script to stay resident, which sounds like mod_perl.

Update: Oh, and you can also read all the answers you go the last time you asked this question here: developing a intranet messenger system. :)