There she is!!, in which a female rabbit falls in love with a male cat. The interspecies part of their relationship plays a big role in the plot: Such romances are extremely frowned upon in their societies (a metaphor for the strained relationship of Japan and Korea).
Happy Tree Friends: Considering that most of the characters are different species, this was inevitable. The Official Couples are Cuddles (a rabbit)/Giggles (a chipmunk) and Handy(a beaver)/Petunia (a Skunk), and a lot of people ship Flippy (a bear) with Flaky (a porcupine).