The Strong Bad Emails used to run shorter, often consisting simply of Strong Bad reading the email and writing his reply. Later ones usually include extended fantasy sequences, flashbacks, interruptions by other characters, and Strong Bad walking away from his computer to do other things which may or may not be related.
The bonus DVD Strong Bad Email called "Accent" plays with early weirdness, as a fan notices that Strong Bad used to have a Mexican accent (likely related to his masked luchador look) and wonders if he ever will get it back. It's even extrapolated to show what his voice may have sounded like five years in the future, had his decline in his accent continued.
Older toons on the site generally ran shorter, a reflection of the Brothers Chaps' inexperience in using Flash. This has resulted in the disparity that newer "Shorts" frequently run longer than the older "Big Toons".
Heck, look at the first few cartoons. "Marshmallow's Last Stand" has some pretty odd animation and character designs, and most of the characters themselves behave differently than in later videos.
Also, Puppy wouldn't develop his sex-crazed personality until Episode 2. He wasn't even in the part of Episode 1 with the naked chick.
The pilot of Happy Tree Friends from way back in 1999. None of the regular characters appear, though the characters in the pilot do somewhat resemble some of the ones from the rest of the series; and the episode was less than a minute long. The opening and end sequences were also completely different from all later episodes. Also, the head of a decapitated character bites someone, which would never happen in the current show.
Neurotically Yours in the first handful of episodes was very rough and different compared to the rest. The animation quality was very rough, Germaine was a Flat Character who didn't speak, Foamy spoke very fast and said whatever was on his mind, and was more of an actual humor-based cartoon with original jokes and scenarios, compared to the more sociological rants seen today.
The Madness Combat series didn't start out so mad, or combative for that matter. The first in the series was about a silly cannon ride that shot people into a giant marshmallow. There were a few deaths in it, but all of them were by accident. The second was an unnamed protagonist just trying to dance the "Chicken Dance," and most of the violence was fisticuffs, though the seeds of the ultra-violent gunplay were sewn there.
The first five episodes of The Frollo Show were written as YouTube Poop rather than coherent narratives. The first five episodes were re-cut into a single video, eliminating the nonsensical scenes and only keeping scenes important to the story. Among the weird differences of the early videos include:
In her initial appearance in the first episode, Frollo wanted to rape Madotsuki. In later episodes, she is a valuable ally to Frollo, and played a key role in launching the events of the second saga, "Frollo Finally Does It".
A lot of Frollo's sentence-mixed dialogue was hard to understand and had to be subtitled. Recent episodes replace this with sound clips of Megabyte from ReBoot, who was also voiced by Tony Jay; both performances sound identical, allowing seamless blending.
In the first two trailers that introduced RWBY, both Ruby and Weiss only showed small signs of emotion, leading many viewers to conclude that they were both Emotionless Girls. Once the series started, it was very clearly established that neither of them were very emotionless at all; Ruby is a slightly oddGenki Girl and while Weiss is a Defrosting Ice Queen, she's still very expressive. Word of God was that the first trailer was more of a "weapon resume" that was meant to demonstrate Ruby's fighting abilities, not her character. In contrast, Blake and Yang have more or less the same characterizations in their introductory trailers as they do in the series.
The first volume showed background extras as black silhouettes without distinct designs. Improvements made for the second volume have remedied that.
In general, the trailers have a very melancholy and desolate tone, contrasting sharply with the series itself, which has its sad moments but is generally upbeat and silly, at least until Cerebus Syndrome hits hard in the latter half of Volume 3. To a lesser degree, the first half of volume 1 heavily uses over-the-top gags like Ruby becoming a chibi version of herself when excited about the weapons and Weiss's voice being sped up to the point of incomprehensibility when reading her Dust safety pamphlet to Ruby. While these gags are still used, they're a lot rarer and more dialed-back now.
The animation and graphics are much more primitive way back in Volume One. For instance, in Volume One, Episode Two, there's a scene where Ruby causes a bunch of Dust to explode giving her the temporary nickname "Crater Face", where there's no craters around her at all. Flash forward to Volume 3, Episode 3 and watch as Winter and Qrow's fight do leave craters.
Early on Yang was implied to be very popular and had a bunch of faceless friends she ditched Ruby to go hang out with upon their arrival. Once the teams were formed a few episodes later Yang exclusively associates only with the other important named characters from then on.
Sun is introduced in the finale of Vol. 1 as a guy who seemed to be living on the streets, arriving in Vale via stowing away on a ship, stealing food, and generally being a loner. Come Vol 2 not only does he stop stealing but it's revealed he's a student at another academy with his own team and is a hunter in training as well, making his initial actions unusual. Why did he ditch his team and why did he need to stowaway to get to Vale when his school was coming a few weeks later anyway?
YouTube Poop as a whole has evolved. Early poops were little more than stuttering the video, reversing, speeding up, or slowing down a segment, or splicing in a meme such as "lotsa spaghetti" mid-sentence. As video editing software evolved, so did pooping, leading to more advanced and polished techniques such as sentence mixing and YTPMV, and even poops with their own storylines.
A good example of this is ChickenPika. His early poops were based on Mama Luigi and the CD-I games, with random memes like "Bombs" spliced in. After deleting most of his old content out of Old Shame, he switched to Michael Rosen sentence-mixing.
Red vs. Blue had its first episode outright mention the Master Chief and that Grif signed on to fight aliens and not get stuck in the middle of nowhere (Later seasons heavily imply that he's a conscript). Also, many of the early episodes had Church and Tucker just spying on the Reds via sniper gun.
There's also things such as Grif arguing with Simmons about him not wanting to go the the "Vegas Quadrant." For starters, this implies that Grif and Simmons were friends before signing up for the military, as opposed to being stuck together and becoming friends out of necessity (Simmons was entirely unaware Grif had a sister until she showed up in the canyon.) There's also the use of the term "Vegas Quadrant", as the writers weren't fully running on Rule of Funny yet (If the joke had been told in a later season, they would have outright called it Las Vegas.)
The first episodes of Inanimate Insanity look drastically different than later episodes (not to mention the fact that MePhone sounded exactly like Chris McLane). When it was released, the fandom thought that it was a terrible attempt to emulate the earlier Battle for Dream Island. With time, the show found its own way and, together with BFDI, made way to numerous "object shows".
The earlier artstyle of II is made fun of in its one-year anniversary, where MePhone changes the artstyle back to what it was back then, with MePhone's voice being completely recycled from those earlier episodes. Everyone hated it.
Pixel art animator Paul Robertson's very early work Hyper Parsnip Bitches has all the character being voiced and, since it's mostly a spoof of anime and videogame tropes, has the two leads speak with an annoying pseudo-Japanese accent. He wisely choose for all his subsequent works to keep the characters silent and let the images speak for themselves.
In a 2001 Ramyun Boy (a South Korean series of flash animation for children that was popular in the early 2000s) episode, the titular main character and his female counterpart look different from their final appearances. Examples are Ramyun Boy looking more chubbier and Ramyun Girl having visible hair.