If the problem is that having multiple recipients polling your system every second is resulting in too much load, you could turn the system upside down and make it a server push system instead, where each client's application just sits there listening on a port for a message to be forwarded. Your server could poll a client to see if they're reachable, and if so, push the message their way. If not, then store the message in the database until the user does log in. On your server side you'll have to operate a small daemon also that receives logins from the clients, and upon login, pushes any stored messages to the client. The same daemon could receive messages from logged-in clients.

I don't know a lot about intranet messaging systems. But it does seem to me that it would be a lot lower load on your server if it operated in a sort of push mode rather than in a mode where each client polls once per second. On the other hand, POP servers handle with grace and ease the fact that email clients (potentially thousands of them) are polling at user-defined intervals that could be very short. So maybe that's not such a bad arrangement after all. ;)

Do you have any code to show? How exactly is this question related to Perl?