GLava, an OpenGL audio spectrum visualizer for X11, had a new release yesterday which includes improvements like FIFO support, support for disabling shader passes through GLSL, along with other enhancements and bug fixes.
GLava can be made to look as a live, animated wallpaper that's in sync with your music. While the application itself does not replace your current wallpaper, GLava can be made to appear as if it's embedded in your desktop background, so you can use it as a real-time audio visualizer on top of your favorite wallpaper. A video demonstration using multiple GLava instances can be seen here.
This is done by options in GLava that allow hiding the application borders, and to allow clicks throw the Glava window, making it behave like it's part of your desktop background.