A penny is a one cent piece minted by the U.S. treasury.
Relevance to Scrubs
On J.D.'s second day at Sacred Heart Hospital, he comments to the Janitor who is repairing a door that it could be a penny that is stuck in the door. The Janitor then tells him "If I find a penny in there, I'm taking you down." Later, the Janitor shows J.D. that it was a penny, and says "I'm watching you!" ("My First Day")
Later on in "My Bright Idea" the allusion of a penny even gave J.D. a bit of relief: Turk offered the Janitor five dollars to eat a penny that was actually a tracking device used by J.D. and Turk to play an advanced variant of hide & seek.
In another season and episode, J.D. sets the Janitor a riddle to do. "What two coins when put together makes 30 cents, and one of them is not a nickel." The Janitor responds after researching at the library - a penny, and an out of mint coin which cost 29 cents to a collector. J.D simply tells him "A quarter and a nickel, because only one of the coins is not a nickel. The other one is." ("My Lucky Night")
In "My Musical", the Janitor sings (in The Rant Song) "It all started... with a penny in the door." Later in "My ABC's", the Janitor says he only hates people who wrong him like taking his things or putting pennies in doors. Both of which he has accused J.D. of doing.
In "My Finale", the Janitor reveals that he kept the penny for 8 years, and uses it to attempt to get J.D to admit to jamming the door on his first day. We learn that the penny fell out of J.D's pocket into the door, which caused the jam.
- J.D. has a fear of pennies, possibly due to this event.
- The penny that the Janitor shows J.D. in "My Finale" has a date of 2006 (despite Scrubs starting in 2001, when the Janitor would have gotten the penny), so his claim that he kept it for eight years might just be another of his wild stories.
- In "My Finale", J.D. says he dropped the penny on his first day but it was actually his second day. However, this is probably due to it being 8 years later, J.D. probably forgot the specific details.