What are the differences between waste gate sizes? 38mm 46mm 50mm etc. Is it just spring rate which allows you to run a certain amount of boost? How do I know which one to get?

 

The openings are actually larger, thus the need for a larger flapper. You can get an internally gated turbo with a 38mm flapper. These allow for more exhaust released and helps keep boost creep down, like on EVO3 16Gs. Boost creep is usually associated with low psi though, say 12-16psi. So, if you boost at 18-21+psi on an EVO316G, you don't really need a larger flapper.
Anyway, larger flappers are good for low boosting and you shouldn't go with small flappers with larger turbos anyway. Flappers have to stay relative to the turbo size. Anything over 400hp capable turbo, I wouldn't use an interal wastegate, you can, but I wouldn't.