Not sure the name of the building, but it's at Epcot on the left hand side as you are leaving future world and walking to world showcase. i think they do special events in there. it's the one that is weirdly shaped and has the walkways over the water. clean and quiet.
That's the Odyssey. There are actually two sets of bathrooms there. The larger one is on the Mexico side of the building, and is right next to First Aid and the Baby Care Center. There's another lesser-used one on the Test Track side that I just "discovered" last year.
Someone already mentioned the ones near Character Connection and the now-former Epcot 25th Anniversary Gallery, which would have been my vote for one of my quietest bathrooms, especially after Character Connection closes.
At the Epcot entrance area, there are bathrooms outside the gate on the Kennel side. I've never actually been in them, but they get a LOT less foot traffic than the ones on the side toward the bus stops.
Up until the wand came down, the bathrooms on the East side of the Spaceship Earth entrance (behind the gift shop) were a lot less busy than the Camera Center/lockers side. But now that the wand is down and doesn't block them from view, they've gotten a bit busier, especially at closing time.
The bathrooms at the International Gateway don't get a lot of foot-traffic. (I'm just blanking on whether they're inside or outside the gates)
At the Studios, there are so few bathrooms, and many of them do double-duty (such as the ones in the ABC Commissary also being the bathrooms for the Sci-Fi), that there aren't many that are low-use. I think there's a set outside the gates to the left, down near the Kennel.
At Animal Kingdom, the bathrooms at the back of Restaurantosaurus are much less crowded than those near Dinorama, unless you're there at a peak meal time.
And while we're on the subject of bathrooms, if there's anywhere in WDW needs MORE bathrooms, it's definitely Future World East. There is only one set of bathrooms for that entire side of FW, on the outside edge of Innoventions West near Test Track. (There were bathrooms inside Wonders of Life, but with the pavilion closed, they don't do much good) There should definitely be another set down toward Energy. (Especially for those who come out of Energy and have been holding it for a while... They should be right there!)
And on my list of "should be expanded" is definitely the ones between Canada and World Showcase Plaza. I don't know about the women's room, but the men's room has one stall and one urinal. Not very high-capacity.
-Rob