Pokémon Diamond and Pearl beta
During the planning and development stages of Pokémon Diamond and Pearl, several parts were going to be a part of the games. Some of them were dropped or changed, but some of those dropped concepts of the beta version can still be found in the game's programming.
Shellos and Gastrodon
A interesting third form of Shellos and Gastrodon has been found. This form is likely a leftover from when Shellos and Gastrodon were planned to be in Ruby and Sapphire. The beta Gastrodon also has various things pointing out from its head in the battle sprite, but is absent from both the male or female sprites. Although this may also be another "unofficial confirmation" of Pokémon Gold and Silver remakes since its PokéDex data states that its colors and shapes differs from region to region.
Other beta-sprites
There has also been discovered other beta-sprites for Munchlax, Weavile and Cherrim. The Munchlax just seems to be a ripoff from the Munchlax-sprite in Dash. The Cherrim beta-sprite was shown in a early Japanese commercial. It is surprisingly like the final sprite, only with the left leg up instead.
Beta maps
A beta-map of Spear Pillar has been found. This is surprisingly like the 'normal' game's Spear Pillar, but it misses the entrance to Mt. Coronet. Many also thinks that the Mystery Zone found in the Pokémon League is a beta-map.