Fifth generation is definitely my favorite. Black and White are just amazing, before I got them, I would never have imagined that they would be as good as they are. There is alot of things to do in the games, enough for 400+ hours of gameplay (in each game, if you get both), and the fact that they are just the start of the fifth generation does only make the future look good.
Fourth generation takes the second place. Diamond, Pearl and Platinum were amazing games, the perfect games to continue with after playing Emerald. They did also have alot of things to do, enough to keep me hooked for a gameplay time of 1000 hours in total, but even then, I am not finished with them yet. HG/SS on the other hand were not that good, but the awesomeness of D/P/P are more than enough to make the generation as a whole really fantastic.
Third place goes to... third generation. I really liked all the new stuff that were added in Ruby and Sapphire, it took the series to a new level. FR/LG were also excellent remakes of the original first generation, improving with all the new things that R/S added and fixed most, if not all, of the flaws that the originals had. But the real star of this generation is Emerald. The Battle Frontier, and even more awesome additions, made this game amazing.
Fourth place goes to first generation. Today, I would probably not be able to enjoy these games at all if I were to play them. But back then, I found them really great. Spending alot of time on things that would turn out to be better in the future generations... But back then, it was still good.
Fifth and final place goes to second generation. These games just plain suck. They did not improve over first generation as much as they could have done, and the fact that they had two regions meant that these would have less content. Kanto was ruined, and would not be back in its former glory until FR/LG. Johto was not a good region, and has never been either. It lacks all the important and interesting things that the other regions have.