Depending on your definition of “homely man,” a bunch of recent sitcoms probably qualify: The King of Queens, Still Standing, Modern Family, According to Jim, etc.
Do they have to be together? Because they certainly weren’t in the Hunchback and such, especially non-Disneyfied. He loves her, in a creepy way, at least.
Living in Oblivion, although it’s unrequited, and Steve Buscemi has other qualities I guess. Speaking of Steve, Ghost World, although it’s more platonic. For that matter, Living in Oblivion was the first role of a certain someone in Game of Thrones. While Peter Dinklage isn’t bad to look at, Tyrion is frequently described as ugly.
In Mercedes Lackey’s Arrows of the Queen trilogy, there’s a strong love interest story between the beautiful main character, Talia, and a rather homely man named Dirk.