My vet suggested
https://secure.balanceit.com/ which is veterinary endorsed, and is pretty handy to mix different ingredients around and see how this affects the nutrition analysis. However, it is STRONGLY lacking in the sense that it doesn't allow you to add bone-in meats so the calculations are always lacking calcium/phos/etc that I know my dog is getting.
Does anyone know of another website that calculates nutrition analysis that might have more options?