Well, what is is it? Mine is Gen 4.
i would have to say gen 3
Gen 1 or 3
Gen 2 will always be my favourite. I love everything about G/S, the cities and towns, the plot, the animations in Crystal, the mix of gen 1 and gen 2 Pokemon, the gym leaders. I'm in love with Gen 2
Gen 3 is mine.
Gen III. Amazing music, amazing visuals for the time, NOT Team Rocket, and awesome starters.
All five Gens are my favorite. I love it when Game Freak introduces something new!
gen 3 FTW
Going to be one of the few people who says this, but Gen IV. Gen IV had perhaps the most evil of all the evil teams in the series. The Pokemon designs were interesting. There was plenty of post-game things to do. *looks at BW with his eyes squinting* The Gym Leaders were fairly intriguing as well. And the Champion is quite popular isn't she? :p So yeah, Gen IV was boss.
Gen III is a close second.