Tick Tock the Crocodile from Disney's adaptation of Peter Pan. On the one hand, he's a crocodile with a taste for human (in this case Captain Hook's) flesh with razor sharp teeth. On the other hand, he's so goofy-looking and his antics with Hook are so funny that you can't help but find him endearing.
Another Dreamworks example is Princess Fiona as an ogre. Ogres are supposed to be ugly, at least in-universe (compared to most ogres in other fiction, Shrek is quite a good-looking chap), but Fiona is on an entirely different class - the only differences to her human form are basically the green skin, ogre ears, wider nose and the extra pounds that make her a Big Beautiful Woman. Nothing else.
Tim Burton Stop-Motion
Some fans of Corpse Bride consider the title character, Emily, to be rather cute for a rotting corpse in a tattered wedding dress whose eye occasionally falls out.
Scrat from Ice Age probably qualifies with that long snout, big eyes and pointed fangs of his.
Sid is also very weird looking with his wide-set eyes, big nose, and crooked teeth all the way down to his slothy hips. He's clumsy, awkward, and is voiced by John Leguizamo in a tone that goes from normal with a lisp to shrill and girly. Everything about him is absolutely huggable.
The eponymous Boxtrolls from "The Boxtrolls", are little, dirty, gray creatures who wear boxes and only come out at night. They have grubby fingers, large teeth, and eyes that glow in the dark. They are also terribly timid, have very innocent motivations, and have the cutest little voices.