In the sixth season, J.D. deals with the news that he's going to be a father, Dr. Cox worries about how his anger is going to affect his offspring, and The Janitor wonders whether his personal vendetta against J.D. is a waste of time. Also, Elliot decides she too wants children.
It's commendable that as a series, Scrubs has managed to maintain much of its energy and continues to push the envelope on how far it's willing to go with its comedy.
The wackiness reached an obvious limit late in that year, and when the writers tried to dial it back last season, J.D. was no longer a recognizable human being who could work in more down-to-earth stories.