If you are talking about musical instruments, using the serial and/or parallel port is the wrong way. Most modern (electronic) instruments have MIDI ports, which you should use. MIDI is a protocol which is more or less like a 9600 baud serial connection from what I know. Documentation on the MIDI wire format is scarce, Perl modules for MIDI are even more scarce, but maybe you can find some (Linux or Windows) MIDI driver for some of the older soundcards with a gameport on them ...

On CPAN, there is at least the MIDI module and some other MIDI modules for MIDI file formats and a good guess would be that the MIDI wire format isn't that far from the MIDI file format ...

Reading the documentation to the MIDI module, there seem to be drivers for MIDI devices under Linux as well - /dev/midi0 might be where you want to write your MIDI data ...

If we aren't talking about musical instruments, ignore this :)