Here's my favorite secluded and quiet ones...
MK: Tomorrowland Terrace
Since Terrace is seasonal and out of the way AND a few steps from the Plaza's larger restrooms - this is my pick for best in the Kingdom.
Epcot: Imagination
Another attraction that sees little foot traffic, Imagination's facilities are on the far right hand side away from the attraction entrance.
DS: Lights, Motors, Action
This has to be one of the largest and quietest restrooms when LMA is dark or between shows. I've had the place to myself on several special occasions. Avoid during Osborne Lights though.
AK: Undecided.
Downtown: Wetzel's Pretzels
Since the Marketplace is usually crazy during the day and Pleasure Island WAS usually crazy at night, this was my pick.
Waterparks: There are none IHMO. Each have four and usually all are quite busy.