I have fond memories of my Pokemon Blue (WHY did I have to lose it!), but my favorite generation will always be the second, with Gold and Silver. That generation introduced so many new things, the music was great, and the HeartGold and SoulSilver remakes are just gorgeous and I love them. Third generation is probably my least favorite... not sure why.
SoulSilver. There's a reason it's still worth more than Black/ White and Black/White 2. both it and HeartGold are the best Pokemon games ever made. People I know are still buying it, even though there's a new generation with a fuckin' sequel.
Day/Night Cycle, Return to Johto/Kanto, semi-3D rendered cutscenes, You could catch the whole 'Dex, revamped story, and it covered for the monstrosies that were Diamond/Pearl/Platinum.
All that, and every Pokemon could follow you. It had the best of all worlds.
Pokemon Yellow, without a doubt. I also like Gold, but Yellow is better. By the way, I only like the 2 first generations of Pokemon, that is Kanto and Jhoto. I've played the next games, but I don't like any of them.