Aluminum Christmas Trees: Doctor Barber may be both a doctor and a barber, and may be a Mad Scientist, but as outlandish as his character's profession may seem, they were very, very real in Medieval Europe, not too far from where Stormalong would be in history.
"Pun Times with Punsie McKale" features a moment where Flapjack finds himself surprisingly holding his own against Punsie McKale in a pun-off....and then Punsie assaults poor Flapjack with a series of color-based puns as he transforms into a hideous rainbow creature that is so intense it causes Flapjack to faint.
Crack Ship: Yes, there are in fact a number of Flapjack/K'nuckles shippers out there....and let's just leave it at that, alright?
Designated Monkey: Though K'nuckles can be an unpleasant person, some of his more humiliating moments can be either overblown or just uncalled for.
Lolly Poopdeck is quite popular, despite his limited screentime.
Sally Syrup is this mostly to shippers who find her and Flapjack adorable together. The writers attempted to deflate this in her second appearance by making her a lot meaner.
With Chowder, as both shows are centered around excitable young protagonists named after food with older mentor figures, and are often considered to be the highlights of the infamous CN Real era. There's also a little with Sanjay and Craig due to the producer of that show being Thurop Van Orman himself as well as Adventure Time, Gravity Falls, Regular Show and Over the Garden Wall as the creators of those shows all worked on Flapjack before moving on to their own things.
Fans of the show are also friendly with fans of Jimmy Two-Shoes, as both shows are centered around young uber-optimistic, blonde-haired protagonists with lazy best friends, and both live in Wretched Hive Cloudcuckoolands. Both shows aired on Teletoon in Canada and Cartoon Network in Southeast Asia, Australia and New Zealand.
The town they live in is called Stormalong Harbor. Stormalong was a tall tale about a giant who became a sea captain.
Dr. Barber's profession. Barbers were often relied upon for medical treatment such as bloodletting (still represented by the red stripe on the barbers' pole outside their shops) because they were often the only ones with sharp instruments to hand.
Germans Love David Hasselhoff: The series was quite popular in Romania and Hungary and had many reruns. Probably because Romanians and Hungarians love Black Comedy as well as Surreal Humour. They also tend to like stories set in the past. Hungarian dub consists of Woolseyisms..
Dr. Barber is commonly depicted in fanart and fanfics as a pedophile, often in regards to Flapjack. His generally creepy behavior doesn't help.
Memetic Mutation: The scene of Captain K'nuckles being impressed by the dog Colonel doing a backflip has been become a meme, such as it being set to the tune of Shooting Stars.
Flapjack himself is the biggest example on this show. He's an innocent and cheerful little boy who genuinely loves everyone and is very adventurous. He has adorable rosy cheeks and an effeminate voice to boot.
K'nuckles and Bubbie as kids as shown in some of the show's flashbacks.
Nausea Fuel: Stormalong getting infected by the plague. And that might not even be the grossest scene if the "Blood Gnats" episode didn't exist.
Spiritual Successor: The cartoon can be a adaptation of Cabin Boy. Both are about pricey boys who are placed in crazy outlandish adventures in the high seas.
Captain K'Nuckles. In one episode, his love interest left him because she found him unattractive, when in actual fact he's got a very simple, even cute design -that is aside from the frequent Gross-Up Close-Up which may show what he looks like in-universe.
What Do You Mean, It's for Kids?: The series is ostensibly meant for a young audience, and at first glance it really doesn't look like it's not. After a few episodes though, the large quantities of Surreal Horror, graphic Body Horror and dark humor were and still are more than a bit unnerving for its target demographic.