With qmail, it's trivial to pipe received emails into a different program.

This is not always a good solution though. You seem to recommend creating a perl process for every message that is received and piping the message to that process from qmail.This is vastly more resource-intensive than having a perl daemon that already runs with all required modules pre-loaded.

Of course, you could have a perl daemon running and have qmail send the message to that, but what's the point? You need to use a mail protocol for transfer between qmail and the daemon, so it's no less work to write and you might as well leave qmail out of the process entirely.

You also have the problem of what to do with messages your perl process can not or does not want to accept. If there's an intermediate MTA, rejecting the message will create a bounce, which may be superfluous. Running your own receiving daemon you can reject at SMTP time which means it's up to the sender to create a bounce or ignore.

Now if you're talking about a machine that receives mail for multiple destinations and has to deliver mail to mailboxes as well as to the perl process then I agree, use a real MTA (I personally would use Exim and not qmail but YMWV). But that doesn't seem to be what the OP wants to do.