A lot of alternative milks are naturally deficient in protein and calcium, so you might want to check that the nutrition label. I use Soy Milk because I am dairy food intolerant, but can still eat yoghurt and cheese. They don't affect most people with diary food intolerance (as opposed to allergy!)
My little g/son has a soy cheese, and I quite like it. It tastes much the same as real cheese but is loads more expensive.
Below is a link that may be helpful - it has alternatives for dairy. Explore the red links in there, too: www.sparkpeople.com/resource/nutrition_art