One of the programs that are used to generate 3D fractals is Mandelbulber. It’s available for the common O.S. (Windows, MacOSX & Linux).
The very first fractals that were generated run in slow computers (compared to the ones we have today), for that reason time ago only 2D was possible. In the last few years some “aficionados” and fractal forum users began to develop “Mandelbulber”, an awesome software used to generate Mandelbrot, Julia, Mendel and IFS 3D fractals.