Here is a quick rundown of those changes that, while showing the series has grown, don't really mess with its formula. Scrubs: The Complete Sixth Season starts off with Tuck and Carla getting ready to have their child, Elliot seeing a fellow doctor who everyone seems to think is gay, Jordan and Dr. Cox are about to have their second child and, oh yeah, J.D. just found out he got his fairly new girlfriend pregnant.
But pretty much everything else has stayed the same over the years. Dr. Cox still calls J.D. girls' names, Janitor still attempts to pull various practical jokes on our protagonist, there is still the favored taxidermied dog gags and all of the actors seem to interact with each other really well.
So, back to the story arcs of this season. In The Complete Sixth Season, both Jordan and Carla will have their babies, and Carla will experience postpartum depression. The cast will get a new season-long patient in Private Dancer, an Iraq vet who is suffering from short-term memory loss as well as a couple episodes that focus on characters other than just J.D. ("His Story IV" which follows Dr. Kelso and "Their Story" which follows Ted, Todd and Jordan). Elliot's boyfriend will propose to her, a couple of times actually. In that particular episode, everyone asks themselves what it would be like to be married to Elliot (yes, there is even a daydream of Carla and Elliot together).
Then, there is J.D. and Kim's baby and budding relationship. The two decide they will have the baby, but Kim is soon asked to work short term at a hospital in Tacoma. The couple decides that they can handle the long term relationship and when J.D. attempts to get there for the first ultrasound, he brings the rest of the cast along with him. There are a couple of twists and turns in this series following this plot, so I don't want to give anything big and surprising away, but this arc was pretty good and really helps to lead into the show's Seventh season.
One of my favorite episodes from this season was "My Musical" where Sacred Heart gets a patient who, because of an odd brain injury, sees and hears everything in the form of a musical. This is especially comical because there might be a pair of characters talking normally, except for the three or four seconds when the patient is wheeled by them on screen. I have to admit, I tend to like the shows that put a musical episode in them (like Buffy).
Another personal favorite is "My House" where the doctors of Sacred Heart run into a series of odd medical mysteries and Dr. Cox fancies himself a House-like character; heck, by the end of the episode, he even has to use a cane. Anyway, being a fan of House made this show extra fun to watch and it was definitely memorable.
This season is also filled with a bit of tragedy as well when Laverne, a tough-as-nails nurse who has been on the show since Season one, gets into a car accident and the characters are forced to say goodbye to their friend in "My Long Goodbye."
Scrubs, in general, has always been a fairly funny show in my opinion. While it isn't the best comedy out there, it definitely has its moments and I tend to like several episodes in a season a lot. Scrubs: The Complete Sixth Season isn't any different and any fan of the series should definitely pick this boxed set up.