At Berklee College of Music, we recently started a project called Berkleeshares (see berkleeshares.com), where we post PDF excerpts of some of our books, with the sounds from the accompanying CDs embedded in the PDFs themselves.

The way we've been able to keep the audio files small(er) and the PDF sizes manageable is to use Squeeze to convert .AIF and .WAV files to .SWF, making them movies without posters that can be played by clicking on the CD icons within the files. These PDFs work cross-platform in Acrobat Reader 6.0. This is the version that supports EMBEDDED audio/video formats.

However, I'm guessing this same process could help you make files for Acrobat 5, where the audio is linked instead of embedded, if it supports .MOV and .SWF (haven't used the earlier version in a while). The benefit to Squeezing files is that they're smaller, and you can ESC to turn off the sound.

You can e-mail me directly if you have more questions!