This should be easy to fix. The app, no doubt, uses wav files for the sounds. Just open these wav files with something like cooledit and reduce the volume.

There was a non-startling wave file that came with either win98 or an old netscape called 'notify.wav' that I used to use for everything. Now that I use the 'puter for music I have all other system sounds disabled. If you want to try the notify.wav, I can e-mail it to you.