Author Theodora Goss lists her Top 10 Fantasy Love Stories in this article. Among others she mentions Neil Gaiman’s Stardust, Audrey Niffenegger’s The Time Traveler’s Wife and Patricia A. McKillip’s The Riddle-Master trilogy. I was not familiar with all stories, but have heard of most of them and have read some of them.
One of my absolute favorites of fantasy love stories is the one depicted in Hayao Miyazaki’s film version of Diana Wynne Jones’ novel Howl’s Moving Castle. There is a tremendous beauty in the spell-breaking love that slowly evolves between the cursed Sophie and the wizard Howl.