I've come up with three main points as to why this episode is so flippin' amazing.
1. Zach Braff's direction. The stretch/real-time/summary relationships in the directing of the break up scene was absolutely fabulous. The less perfect but still awesome direction of the 'what could have happened if JD pushed Molly's bangs back' was great. Normally I don't like when actor's put their hands in the director's role, but in this case I think Braff did an excellent job.
2. The music choice of "Closer" by Joshua Radin was brilliant and so perfectly fitting for the direction which, as stated above, was creatively above-average.
3. Neil Flynn's performance is so impressive in this episode. His interactions with blonde doctor are so moving that it makes me teary-eyed everytime I watch it. The Janitor is not given nearly as much attention as he deserves for his acting chops, and Neil Flynn's dramatic storyline in this episode blew me away. [This episode is just another reason why Neil Flynn is my absolute favorite actor of all time.]