However, it would be good to do this completely within one Perl application. ... The question then becomes has any Monk used this approach for audio conversion and if so it would be great if some more complete sample Perl code was available.

It doesn't get simpler than convert( $infile, $outfile ); where sub convert does the appropriate system $converter => '--infile', $infile, '--outfile', $outfile ...

http://www.playogg.org/

Searching is easy :D

site:perlmonks.org mencoder -> Convert videos for my iPhone

site:perlmonks.org convert mp3 -> Batch CD track (WAV) to MP3 conversion and tagging

mp3 conv -> Convert FLACs to MP3

?node_id=3989;HIT=mp3;re=N -> re-encode mp3 files, Automatically Encode Ogg / MP3s, starcd2mp3, wscd2mp3