I think the question refers to non-Adult Swim animation. It does seem like Gargoyles comic was suggesting Lexington (who's been creator confirmed as gay) and Staghart (who's described as sounding like Alan Cumming)... STAS had Maggie and Tobey, who were a couple in the comics at the time. Jumbaa and Pleakey for sure.
I'll throw out the names of others who could work as couples in future reboots: Ram Man and Man-E-Faces in He-Man, Spinnerella and Netossa in She-Ra (they're less credible as "sisters" than Sailors U&N are as "cousins"), Jeepers and Vorn from Freakazoid... ok, all of these are 10+ years old and Disney feature animation is bound to be the last to make the leap (It was about 40 years between H-B's reluctant use of Valerie the Pussycat and Disney's Princess Tiana)
Although I haven't seen the Yakitate anime- just read the manga, I have to mention Monica and Kai. On the Western animation front, my current fave is Jonah Hex and Lashina.