In conversational Hebrew, Yiddish and Jewish-English, "Mitzvah" is commonly used meaning a "good deed". How did this transition happen, from a Mitzvah meaning a specific command to meaning a good deed which one is not necessarily commanded and obliged to do? Further, in the Torah the term "Mitzvah" is frequently used in parallelisms together with "Chukkim" and "Mishpatim". Why did the one term undergo such a change of meaning and the others didn’t?

I am not a philologist. In the Talmud, the word Mitzvah can mean two things depending on the context; There is a Mitzvah as appose to an Avera (sin), in that context a Mitzvah is a commandment (e.g. Brachot 6a, Shabbat 21a etc.), And there is a Mitzvah as appose to Chova (obligation), in that context it will mean a good deed (e.g. Brachot 29b, Shabbat 165b, Ktubot 44a, ibid 49b, etc.). Perhaps it evolved from the fact that a commandment is also a good deed and will grant reward to those who perform it.