I was around since the first gen games, and until fourth gen came out, I thought that second gen was best. I lost my faith in Pokemon during the third generation because I felt that R/S were lacking something, and as a result didn't make any more Pokemon purchases until Mystery Dungeon. Then the fourth generation started, and it's definitely the best one yet in my book. I vote for fourth.
I vote fourth generation assuming thats what you count HG/SS under, that was easily my favourite Pokemon game, taking elements from the otherwise best games in the series (Platinum and G/S/C) and blending them into one awesome game.
If it counts as 2nd gen my vote goes to that instead, but I presumed it would come under the 4th generation.