Quasimodo from Disney's The Hunchback of Notre Dame. Once you get past his deformed face, you'd want to do like the little girl at the end, and cuddle him. Of course he's considerably less ugly than he was supposed to be in the book.
Seeing as WALL•E is a rusty, dirty, trash compactor, he certainly qualifies.
And his adorable little disease-harboring pet, a cockroach.
All of the experiments apply. You could also count Jumba and Pleakley, too. And Lilo's doll, Scrump. Let's just face it: Chris Sanders loves Ugly Cute.
Some of the character designs in Dreamworks' Monsters vs. Aliens, like the giant bug monster, Insectosaurus.
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.
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.
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.