The first Teen Girl Squad episode is the only one where the "IT'S OVER!!!" ending card is actually written on top of the last scene rather than on a separate card.
The first Halloween Episode of Homestar Runner (the website the above spun off from) is the only one in which Homsar does not appear (it was released before the second Strong Bad Email ever, which marked the character's debut).
The Strong Bad Emails used to run shorter, and did not go into random segues.
Heck, look at the first few cartoons. "Marshmallow's Last Stand" has some pretty odd animation and character designs.
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. The character designs were radically different; Lumpy was a dinosaur with a Hair-Trigger Temper instead of a stupid moose; and the episode was less than a minute long.
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.