Each color is a version, and each system had a Generation of them. Each one has different Pokemon available, with later games seperating Legendaries to them. For example with the new Diamond and Pearl, you can only get my boy Houndoom is Pearl version, while Diamond holds Scyther to themselves. Each version generally has about 5-10 exclusives, I won't bother listing them all. I am going for Pearl when it comes out just because of Houndoom's exclusivity.
The original Gameboy had the Colored Generation, Red/Blue/Yellow. The original 151 included the starter favorites Bulbasaur, Charmander, and Squirtle. Had the Legendary Bird Trio Articuno, Zapdos, and Moltres. Had the Genetically Engineered beast Mewtwo, and if you went to one of those Nintendo tours they did back then you got the parent of Mewtwo's DNA, Mew.
The Gameboy Color had the Metallic Generation, Gold/Silver/Crystal. Increasing the Pokemon count, it gave birth to many fan favorites including my boy Houndoom, a Dark/Fire type. This generation introduced two new types into the fray, Dark and Steel. The starters are popular but not used pretty much and are the most uncommon of the starters you'll see now adays, Chikorita, Cyndaquil, and Totodile. The Trio of this generation were the Dogs/Cats/Gerbils, Entei, Raikou, and Suicune. The guardian of the Legendary Bird Trio, Lugia, was also available as well as I believe the supposed creator of the Legendary Dogs, Ho-oh. I believe Nintendo never gave out Celebi, this generation's Mew.
For the Gameboy Advanced we had the Jewel Generation, consisting of Ruby/Sapphire/Emerald. Emerald, until Diamond/Pearl come out, is the most played one currently with the most features and Pokemon count. The starters are the commonly used Treeko, Torchic, and Mudkip. For the Ruby version, you had to battle the Legendary Pokemon Groudon, the creator of all the land. Sapphire version got to battle Kyogre, the creator of the sea. In Emerald you had the ability to battle/capture both of them. Also featured was the Guardian of the Skies, Rayquaza. The Legendary Trio consisted of the Regis, Regice, Registeel, and Regirock. The Wish Maker Pokemon, Jirachi, is available to those who preordered Pokemon Colosseum for the Gamecube years back, and Nintendo recently did a tour around the country for Deoxys. Also for the Gameboy Advance were remakes of the original Colored Generation, Fire Red and Leaf Green, so you could get the previous Generation Pokemon for the newer gamers.
Now we are at the most current one, being released in North America on April 22nd of this year; Diamond and Pearl for the Nintendo DS. With yet another boost to the Pokemon count, up to a total of 493, this is the version to get. Every Pokemon from all the previous generations is available in one way or another except for the previous starters and legendaries, so the amount of Pokemon available is staggering. Featuring the starters Turtwig, Piplup, and Chimchar, and the most Legendaries to date, this is the version to get. And of course, Wifi support. Battling and Trading online.
For now I recommend checking out Emerald version until Diamond/Pearl come stateside.
If you have a DS, pick up Diamond or Pearl versions