The API for Properties describes how this works. All Unicode chars can be saved; however if you look at the raw file data you will see that if the chars are outside the ISO-8859-1 range, they are represented using Unicode escape sequences, such as "\u03a9". Which is a little ugly to look at, but you don't have to look at the files yourself. Just use the store() and load() methods;
Java will take care of everything for you, and all your Unicode characters will be properly saved and retrieved.