The first instance of the bathroom being used is by one Mrs. Mia Wallace, in Jack Rabbit Slim's. She goes to "powder her nose" and shows that she has an enormous drug problem, causing her to OD later in the film, starting a long chain of events. As she returns from the bathroom she comments on the phenomena of bathrooms, stating how it is "lucky to have food waiting for her", indirectly addressing the wider issue of how life can change as one examines it through an outside perspective, taking a moment, and that is all that is necessary, to observe one's situation from a decent distance, and to see what changes happen that are invisible to our naked eyes.
The next occurrence is soon after, as Vincent contemplates just what the hell he is going to do with Mia, given they are both high and drunk, and if anything major happens there is a good chance he will be thrown out a window, an occurrence quite explicitly detailed earlier on. Mia unfortunately tries to snort some heroine, resulting in a rather unfortunate situation, and a changing world after only a minute away. This speaks to the film as a whole, as the different disordered segments can be disorienting, when one story disappears only to reappear at a later time. The haphazard nature of all of this still seems very planned, possibly to simulate the eternal clockwork of life and its turns and twists.
The next two bathroom sequences occur in the golden watch tale, that of a boxer who killed a man, and now seeks asylum from all the people out to get him. One instance simply helps to show intimacy between a couple, providing contrast to the rape which happens later, quite an opposite indeed. The other instance close to that one, is Vincent's final hurrah, as he steps out of the bathroom to find his death staring straight at him, as all his past deeds are catching up to him in this single instance of a man with a gun. He realizes this, and wonders just why everything had happened, as the disaster of his life is fully realized, the violence inherent in his profession is truly revealed in his own end, and Jules' interpretation of events may have been right. Wandering the earth doesn't sound so bad compared to the end.
Chronologically this event in the bathroom happened first, but in the film it is one of the last scenes. We have our Jerry Seinfeld look-alike waiting in the bathroom with a revolver "bigger than he is", listening to his friends die, himself dying on the inside. Soon thereafter he charges out firing rapidly, hitting nothing, and finding that his end was inevitable. This however does bring about Jules' reflections on God, miracles, and his profession, so some good did come of it. One life ends, another begins anew, as the world is changed completely, because one guy decided he need to take a piss. This is all best summarized by Jule's misquoting of a bible verse, Ezekiel 25:17, guiding the innocent through the valley of darkness as a Shepard.
The last, and perhaps least significant, is when Vincent retreats to the diner's safe haven, and comes out to find a hold up. Perhaps the most material of all these visits in its end result, it is still a very important moment for Jules, and the beginning of the end for Vincent. By finding these robbers, Honey Bunny and Ringo, we find the insatiable human need for material goods, and what lengths some people are willing to go to to get them. Jules here decides to give all the money away, including that of the other customers, in his attempt at charity, allowing them to live, and perhaps changing the way their lives will progress. Both him and Vincent then exit to the film's eponymous theme tune, and depart, one to his death, and one to a new life, all springing from a few moments which change everything.
So bathrooms seem insignificant in comparison to the larger themes of many works, including this one, but maybe something so necessary and yet glossed over or ignored in near every work is one of the most important. Often the things we forget are the ones which we truly need, evidenced by the Golden Watch, and sometimes the one thing we are searching for we can never truly find, like in Moby Dick. It all comes back to the little things, the unimportant details that mount up to an insurmountable pile of shit, reeking of forgetfulness, and the eternally lost miasmas of life.