The process has been gradual for us. Nudity has never been a big issue (I was raised in a prudish household but have tried to be more relaxed), but I also want my son to respect privacy and have some sense of modesty :)
Basically, when he started developing more than a passing interest in anatomy (his or mine), I'd start adapting. When he was a tot, we took showers together because it was easier and fast; when he started being concerned that we had differnet parts, I explained it matter of factly, but also decided it was time for him to have his own showers, with assistance of course.
When he started becoming more interested in his own anatomy, I started introducing the concept that he could play with himself in the privacy of his own room, but not out where others could see. This was about the time I started training him to be aware that he needed to wear, at minimum, boxers in the house if he was not fully clothed.
So, my guide has been his level of interest and how he interacts with others. I believe in being honest with children, at their conceptual level. I also do not want my child to have the handups I had growing up. It has been a growing experience for us both.
As to bathroom time, I still make him go into the "women and children" bathroom as he is 6 years old. However, he can manage in the stall just fine by himself. ;)