Have you considered using 100% rye bread as your beginning and going from there, rather than pizza crust? Peter Reinhart's Bread Baker's Apprentice has a 100% rye sourdough bread that might suit your needs, although it will be a time consuming process. A preview is online in Google Books. The recipe is similar to a Neopolitan pizza dough - just basic ingredients with no fat. Because of this, I'd roll out the pizza very thin, New York style, for a crackling crisp crust. If you don't want to buy the book, many local libraries carry it in the US, at least.
I'm not sure that's the right way to go about this. There are tons and tons of types of cheeses. I'm not sure you'll find a good list of all substitutes because it will be too big to put together.
Instead, I think you need to learn about the types of cheese so that you can make an informed decision. Is a cheese blue, sharp, creamy, hard, soft? How does it melt? What part of the world is it from? Those questions will allow you to find a cheese that is similar enough to make a good substitution.
For instance, if a recipe called for Pecorino a hard Italian cheese, Parmesan (another hard Italian cheese) would make a much better substitute than goat cheese or cheddar.
So see what cheeses are available at your local store. Write down the whole list (and preferably buy some of each). Get home and do a little bit of research on each one. Where is it from? How do people describe it? Take some notes on all of this. Then, when you see a new cheese in a recipe, look it up and see how it's described. Then find a cheese from a similar area with similar characteristics, and you should be good to go.
Edit: While I stand by my approach as a great way to go about this, I did find a good resource. Cook's Thesaurus has a great list of cheeses, including substitutes, broken down by type of cheese, type of milk, hardness, etc.
Best Answer
Pizza hut uses skim milk mozzarella on it's pizza, at least in the USA. Not sure what they use in other countries, but I would imagine it is still the same. Skim milk mozzarella is extremely stretchy, but loses a little on the flavor end. More expensive pizzerias normally spring for the full fat mozzarella cheese.
Dominos uses a mix of cheese, made up of mozzarella, Pecarino, Parmesan, and asiago cheeses. I think in their most recent reboot they switched to part skim mozzarella but I am not one hundred percent on that.