Audio::Play and SDL can both play sample files in a fairly portable way. Audio::Play can also take a buffer of generated samples. I'm currently working on a module that can generate all kinds of audio streams, but it doesn't really have as simple an interface as Audio::Beep.

If you want to experiment, you can also try my very new Audio::PortAudio module (should be on CPAN soon - i uploaded it 2 hours ago). It does more or less the same thing Audio::Play does, but also does input and multiple channels.