Beta Pokémon Games are the first trial games. Since Generation I there has been many beta versions of all the games. There can be some notable differences when looking at the beta versions and the officially released versions.
With the first games having taken so long to develop (Six years in total) Pokemon Red and Green was released. There were however some beta versions of the games found through various glitches. The most well known one was Missingo. It was also discovered that the producers had originally intended that the player be able to battle Professor Oak. But it was most likely scrapped due to timing, but players can glitch the game in order to actually battler him.
Generation II was the most thoroughly covered games. A beta version had a few Pokémon that were later scrapped. Initially Ledyba was slightly gray-ish, there was to be a Pokémon resembling a turtle (It resembled Tirtouga), a Pokémon resembling a mix between Clefairy and Tyrogue that had a similar form to that of Hitmontop, Tyranitar initially was going to be slightly lighter and had its arms similar to Nidoking's, there was also to be a different female trainer the player had the option to choose. There was also a trainer that was scrapped in the official release. The beta name wasn't even Pokémon Gold and Silver it was Pocket Monsters 2. There were many prototype towns/cities. Goldenrod City was drastically changed in the beta version, Ecruteak City was originally meant to have a medicine shop instead of Cianwood City.
The player's hometown was first called "Silent Hills". Maps were a bit incomplete after post-release, they showed what most of Johto looked like when it was still in development. The Safari Zone was also very different in the beta version. A woman also refers to a pharmacy in Ecruteak which was possible that the pharmacy was meant for Ecruteak. Cinnabar Island was originally going to have a lab like the previous generation. It wasn't intended for the island to erupt. There was also text of mentioning Sweet Honey. It was scrapped but it did return in Generation IV.
Lots of changes happened during this generation especially with Pokémon Ruby and Sapphire. Route 104 was playable in the beta version (Pokémon Festa 2002), the Pretty Petal shop was also noted as being "Not Yet Open". It is also notable that Sharpedo possibly didn't have an pre-evolutionary form because it was at a very low level. Sharpedo also didn't have an ability. In early shots there were Pokémarts that had the same colored designs as Pokémon Centers. There was also supposed to be wild double battles but the idea was scrapped later on but it did return in the 4th Generation. There was also a weather effect which was snow. Albeit only 3 snowflakes came at a time it wasn't used.
Originally, there were quite a bit of Pokémon that were designed differently. Two concepts of Torchic were made, one had Torchic in an eggshell (just as Togepi) another had Torchic with a flame symbol on the backside of its head and big ears. There was also a few scrapped versions of Treecko. There was also a prototype Latias/Blaziken , Groundon was also altered a bit. Gastrodon was originally meant to appear in Generation III but was moved back to Generation IV.