i'd say the rarest tamagotchi characters are the secret ones. some of the secret characters didn't have names until very recently when bandai released them.
toratchi: looks like a tiger.
hatenatchi: looks like a whale with a heart for a tail.
flowertchi: looks like a flower growing out of the ground.
butterflytchi: looks like a butterfly.
oyajitchi: looks like a middle-aged man. you get this character right after your tama is a toddler, because it magically skips the teen and adult stages.
so far, these are the ones i consider more rare than the others.