How to lower the volume of Skype sound effects?
What you can do is to disable the sound effects, for each individual "event" (incoming call, new message received, etc).
Or, even better, you can associate to each event a different sound effect, maybe with a different volume.

To do this, you need to go to the preferences, and choose the "Notifications" panel. Then, you choose each individual "Event" for which you want to turn off the sound (via the first drop-down menu), and turn it off by means of the "Play sound" check button.
You can also choose a different sound effect (maybe with a different volume) by choosing a different audio file. This is done using the drop-down menu next to "Play sound", and selecting the last option: "Add/Remove...".
You can then select your file using the "+" button on the bottom-left corner of the small pop-up window.
To have different volumes you will need to create/edit the audio files, and change their volume, before you associate them to the Skype events.