Nightcrawler's demonic appearance doesn't exactly falls under the classic definition of "beautiful", yet he's one of the most appreciated Mr. Fanservice among the X-Men; he's basically the male version of a Cute Monster Girl. Classic Excalibur artist/writer Alan Davis may have something to do with this. Originally, Dave Cockrum designed Nightcrawler to look pretty scary as a contrast to his out-going personality (in fact, his very first design was some kind of bat-creature and was so spooky, Marvel nixed the idea). Alan Davis decided to turn him into a handsome swashbuckler type modeled after Errol Flynn.
Shuma-Gorath, a Captain Ersatz of Cthulhu and one of Doctor Strange's minor foes (Minor as in he doesn't appear very often. He is, however, literally an evil god), is a huge, one-eyed squid thing that somehow manages to look huggably cute. His Marvel vs. Capcom design shrinks him down to human size and makes him look positively shy.
Many fangirls consider the "fascinatingly ugly" Walter Kovacs, AKA Rorschach, the cutest character in Watchmen. This may be more in North America's fandom versus Europe, as the ginger haired appearance carries a more negative connotation across the pond compared to in Canada and America where the awkward appearance is often considered to be rather sweet and endearing.
The Loathsome, a story from EC Comics, is about a girl who was born mutated by atomic radiation, so much so that the doctor tells her mother she was stillborn and ships her off to an orphanage where she's abused because of her appearance. But when she's finally shown◊ near the end of the comic, she's not nearly as hideous as she was made out to be. Alex Ross used her as the basis for Maggie in Marvels.
Sola with her enormousNonmammal Mammaries (though since the Red Martians, indistinguishable from humans except for skin color, are also oviparous, both species may be monotremes as opposed to true non-mammals) in that same work could qualify as well, though she may be more in the Cute Monster Girl category.
The gay demons in the Chick Tract, "The Birds and the Bees".
Lockjaw, the giant pug-like pet dog of Marvel's Inhumans. Although the size of a hippo, he's as cute as any pug. It's also sort of weird, since at one point it was suggested he actually is an Inhuman who simply got hit with the ugly stick very hard by Terrigenesis. This was retconned later... re-creating the plothole as to just where the Inhumans got him anyway (Terrigenesis does not affect animals).
Pooch the Lowbeast from Hack/Slash. He's superficially hideous with his protruding jaws and cloven hooves, but his loyalty to his masters and his desire to be petted and loved like any ordinary dog make him adorable.
Jim the Cave Troll from My Little Pony: Friendship Is Magic (IDW). Sure he's a hulking brute who could easily crush a pony if he wanted to, but he's so innocent and carefree it's hard not to see him as anything other than the softie he really is. And he genuinely did love the Mane Six's company.
The uncorrupted moon bunny in Issue #7. Fluttershy certainly thinks so.