Could there be a sound effects menu where we could select which sound effects we want? The most effective sound effect is the one that lets you know when a script is done, yet all the other sound effects get annoying. maybe a sub-menu.
For things like sounds effects and images, you can always control them manually by changing the resources files. If you go to your Foldit install directory (where the foldit executable is) you should see a folder called "cmp-resources-". Go into there and then into "resources/sounds/"
You can paste in some dummy .ogg files to replace the sounds you don't like.
One note, this is kind of a hack so it will not persist whenever Foldit updates the resources. Your changes will be overridden.