This is something that keeps coming up lately, so I think it's time we finely let the community just vote on it.
The argument is simple: What is the true Third Version to Generation I: Blue Version (JP) or Yellow.
Blue Version was the third Pokemon game released in Japan in October of 1996. It was a minor revision to the original Red and Green versions that were released earlier that same year, and was originally only available to subscribers of CoroCoro. Blue had the same story as it's predecessors, but offered a slight update to the graphics and sounds from the original two versions, and also fixed several known glitches. When it was time to start releasing Pokemon in other regions, the original Red and Green versions provided the version exclusive lists, but Blue provided the graphics, game engine, and script for translation.
Yellow Version was released in Japan in September of 1998. Yellow was originally intended to give GF time to do some re-tweaking on the at-then upcoming GenII games. It was the fourth game released in Japan, but was the third game released world wide. While Yellow followed the same basic storyline as the other Generation 1 games, there were a few key differences that set it apart. Instead of choosing between Bulbasaur, Charmander, or Squirtle at the beginning of the game, the player is given a Pikachu. The player's rival receives an Eevee as his starter Pokemon, and chooses it's evolution based on the outcome of several early game battles against him. The other three starter Pokemon can be received about a quarter way through the game after certain conditions have been met. Jessie and James from the anime have several appearances throughout the game and can be battled. Also of note, level-up and TM compatibility were changed slightly. (This was actually the first game in the series where Charizard could learn Fly.)