I'd say that my favorites are either the restrooms by Pirates or Tangled. Tangled always seem to have availability, unlike the resort hotels. My alltime favorite restrooms onsite are on the second floor of the Contemporary back by the convention center. If no conventions are underway, you basically have the entire place to yourself.
The Magic Kingdom was a close call one time. I got onto Pirates and noticed a very bad disturbance in the force occurring. I prayed as well as lying down in my wife's lap while hoping that the boats weren't stacking. I exited the ride in the biggest hurry of my life. Sadly, I did not know the MK layout well enough, hadn't memorized restroom locations, and missed the Pirates restrooms. I hurried (as much as you can when you're heel and toeing it) to the old restrooms by Peter Pan. Nowadays, I maintain a steady remembrance of where each one is and even am ready to check the app. It must be popular to do since the app has a selection solely for restrooms.
This thread is awesome. In fact, I love it so much that I'm ranking it both #1 and #2.