Learn Croatian: Što je to?

It is neuter. Just like regular nouns that end in -o or -e (like selo or more), the pointing word to is neuter singular. You use it when asking about an unknown object, because when you don't know what something is, you automatically default to the neuter gender.

I sometimes hear people say šta instead of što. Are they the same?

Yes, they mean the exact same thing. Što is the standard, formal word for "what", which you will see in writing and textbooks. However, in casual everyday speech, many people say šta. It is good to know both, but sticking to što is the safest bet while you are learning.

Why is the word order Što je to? Can I say Što to je?

You must say Što je to. The verb je is a type of word called a "clitic", which means it is a short, unstressed word that strongly prefers to be in the second position of a sentence. Because of this strict rule, it jumps right after the first word, Što.

If to means "that", how do I ask "What is this?"