If you are looking for a truly to scale animation of our solar system, I suggest you quit. The distances between planets/the sun is simply too great, everything would have to be shown far smaller than a pixel to fit on a computer monitor. Not to mention if the kuiper belt and oort cloud are to be included.
If you are ever in Australia, drive from Sydney to Connabararbran (it's about a 5-6 hour drive I think). Along the highway is a scale model of the Solar System. Jupiter is several metres in diameter, so at this scale most of the planets are many kilometers from each other along the side of the road.
Okay so it's not a website, but it really gives you a seen of the emptiness of the Solar System! Plus once you get to Coona you can check out the Anglo Australian Telescope, the first telescope to do a really serious galaxy reshift survey (the 2DFGRS) that told us so much about what we know about cosmology today.