If you're an application author and you want to install sounds so that they can be used by your application, you should at least install the sound file in the "freedesktop" theme. This means installing a stereo WAV file in $XDG_DATA_DIRS/sounds/freedesktop/stereo/.
Optionally you can install sounds in different formats and languages. For example, installing a localized OGG/Vorbis 5.1 game sound in $prefix/share/sounds/freedesktop/5.1/fr.
You might even want to install sounds that match other well known themes so your application will fit in with some specific desktop environment.
It is recommended that the sounds installed in the freedesktop theme sound neutral, since it is a fallback theme that will be used in combination with some very different sounds from any origin. But if you don't have any neutral sound, please install whatever sound you have in the freedesktop theme so that all your application can at least produce some sounds in all themes.
After installing/updating a sound in a theme directory, make sure to update the mtime of the theme directory itself (i.e. touch $XDG_DATA_DIRS/sounds/freedesktop or similar), so that caches can be kept up-to-date.