Every 3rd gen game was absolutely excellent.

Ruby and Sapphire to this day have the best soundtrack, a beautiful region with pokemon that fit perfectly into their habitats, and really stepped up the game as far as the plot goes (compare Team Aqua and Magma to Team Rocket). It also gave us pokemon contests in their original and best form, and none of the other little side quests since have topped the Hoenn contests.
Pokemon Colosseum has the most epic plot of any pokemon game, also some great music found within, and (I thought) did a great job integrating the actual colosseums into the actual game, while still having a mega-challenging tournament mode. The first real 3D world and the rich vs poor dynamic also make this game really stand out from anything that has come after it. Only downside: the fact that you cannot by any means have more than 48 pokemon on the game at once. BUT you get to play as a 3D Brendan or May in Mt. Battle, and there is nothing cooler than that.
Firered and Leafgreen take the original game and make it better in pretty much every single way. We finally get to see a modern style view of the Kanto region, and the Sevii Islands post-game areas did a really good job (for me, at least) at making you actually want to catch every new pokemon that appeared. They also gave you the first wireless trading, which was a godsend for people who didn't want to have to worry about holding the gameboy 100% perfectly still and holding in a link cable and hoping it didn't disconnect for no reason. Only downside: being locked into the regional pokedex for so long - I remember my Golbat trying to evolve several times.
Emerald Version is a rehash of your Hoenn journey with more available pokemon and a more in-depth plot. But the real crown jewel was the Battle Frontier, which was such a new concept and completely passed up every single other post-game activity in the other games with the possible exception of Colosseum's Battle Mode. But damn, the Battle Frontier was amazing when it first came out, enough to make my brother and I actually share a game to be able to both access it. And that's saying something!

(I unfortunately never got the chance to play Pokemon XD. They did fix the limited amount of pokemon problem, and added several new areas, so I might have enjoyed it)

With the combination of Ruby/Sapphire/Colosseum/Firered/Leafgreen/Emerald you don't really need any of the other pokemon games. I never bought any more games after this, because for me the third generation was and still is THE pokemon world.

There's no way I can single out one of the games as the best, because they were all absolutely excellent in almost every possible way.

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