Dr. Maddox, played by Courteney Cox, makes fun of Dr. Perry Cox's last name.
It is revealed that The Janitor was in The Fugitive. Neil Flynn, who plays The Janitor, really did play that role.
A very dark one - you know that episode where Hooch threatens to run somebody over? Guess which actor actually had fatally run someone over in the early nineties. Go on. Guess.
In "My Last Chance", JD is watching Sixteen Candles (starring Molly Ringwald) with Dr. Molly Clock and internally exclaims "God bless Mollys everywhere!". That particular episode featured an ambulance driver played by Molly Shannon.
In "My Last Words", Turk tells a patient about how he used to be a football safety in college. Guess where the character played by Donald Faison, who played Turk, ends up playing in the movie Remember the Titans? He starts out on offence but is moved to safety.
In Season 9, Lucy mentions that Dr. Cox used to be roommates with Michael Bolton. Dr. Cox shoots back that he hates Michael Bolton.
In My Cold Shower, during Dr. Cox's imagine spot, he holds a knife the same way as John C. McGinley character Edgar Vess from Dean Koontz's Intensity miniseries
Channel Hop: Moved to ABC in the 8th Season. Interestingly enough, the show was ABC produced anyway but aired on NBC. This was because the show pre-dated a change in what incentives each network looked for in a show. In 2001, it was more common for networks to buy shows from each other's production companies (though usually only after the network that technically produced it passed. This is true in the case of Scrubs: ABC originally declined to air the show), because the only way to profit off a show was through the network charging for commercial time (how much they charged was based on ratings), and an eventual syndication deal, through which the production company and the broadcast network would split the profits. By the mid-00's, broadcast ratings were down across the board (meaning networks couldn't charge as much for ads), but the DVD and online markets were rising. Only production companies made money from the DVD and online download sales. This was the tipping point at which networks started to only broadcast shows made by their own production companies, because then if the show didn't have great ratings but had a strong cult audience who would buy the DVD's, the parent company of both the network and the production company would still profit.
Creator Couple: Series creator Bill Lawrence and actress Christa Miller (Jordan Sullivan); the wedding video Dr. Cox watches in My Bad (Jordan's first appearance) is actually Bill and Christa's, which is why only Christa can be seen.
Directed by Cast Member: Zach Braff directed 7 episodes during the show's run, including the 100th episode. He also played a major role in the music used for the show; one of the biggest strengths of the show.
A lesser known example: Michael McDonald of MADtv fame guest starred as a patient in 3 episodes before directing 6 episodes in the later seasons, some of which he acted in. This eventually led to him being hired as a consulting producer, staff writer, frequent director and sometimes actor on Bill Lawrence's next comedy series.
Executive Meddling: After Masi Oka joined the cast of Heroes, and Scrubs moved to ABC, Oka was point-blank told by NBC execs that if he continued to make guest appearances on the show, he would be fired from "Heroes". Despite the fact that they allowed many of their other actors to continue making guest appearances on other shows, even on other competing networks. Obviously, this was NBC just being petty over the show switching to ABC, despite NBC's own treatment of the series.
Reality Subtext: In the episode "My Catalyst", Michael J. Fox plays a doctor with OCD - a neurological disorder that all-but usurps control of the body from the active portions of the head - played by a man diagnosed with Parkinson's Disease, which accomplishes the same thing in a vastly different way. In an interview after that episode aired, Fox stated that he allowed his frustration with Parkinson's to help inform the character of Dr. Casey.
Science Marches On - Dr. Townshend's episode hinges on his use of an old treatment instead of the much safer modern alternative. As Dr. Kelso tells him, even the newest doctor's education is obsolete within five years.
Throw It In: After realising Neil Flynn was a great improv comedian, the writers began to write most of the Janitor scenes with the simple direction "Neil says something".
The Outtakes definitely attest to the fact that often the crew had no idea what he was going to say in any given take.
Had the series been cancelled at the end of Season 1, the Janitor was going to be revealed as a figment of JD's imagination. (This was foreshadowed by the Janitor only interacting directly with JD and being seen by him... barring a few rare moments.) This intention was continued early into Season 2, but Neil Flynn's insistence that he get to act with the other cast members (and consequentially be given more to do) reversed it.
Neil Flynn was contracted to return in Season 9 as a cast member, but only if he didn't find a regular role somewhere else. Had The Middle not been picked up, Flynn would've been a regular in the final season.
During one of the later seasons, there were conversations had about bringing Arrested Development analrapist Tobias Funke on as Sacred Heart's in-house shrink. It ended up being too complicated to work out a deal with all the parties involved.