Black and White 1 and 2
Because of N basically.
I'm going to be very boring and say Gold/Silver/Crystal. In my case, specifically Silver.
I think one of the main problems I have with the later games, which I've played and continue to enjoy (I finally got around to playing Pokemon Black last month), is there are too many Pokemon. The designs are still reasonably imaginative and interesting, but I don't think they have the same quality, by and large, as the first 251. In addition, I'd also say that 251 was a much more manageable number. With 251, I was more excited because I believed that I could actually complete my Pokedex, because realistically there were only four games I'd need (or ideally, one friend with Blue/Gold while I had Red/Silver).
I also liked the variety of locations. I really quite like Kanto as a region - its towns, gym leaders and locales are all reasonably close to my heart. I especially liked the ability to visit both Kanto and Johto - something I've wished subsequent games would let you do. While it wasn't quite like getting two games in one, it provided much more to do after beating the Elite Four. Generally I find that in the Pokemon games I lose interest after beating the Elite Four - G/S/C kept me interested. 16 gyms also gave you the need to have a well-rounded Pokemon team. I tend to use the same Pokemon the whole way through the game, rather than switching based on my needs, and so it gives me an extra incentive to need to have a team that can cope with any situation.
The games also introduced a number of innovations which I liked - things like the PokeGear, shiny Pokemon, legendary Pokemon you have to chase around, day and night, events throughout the week, etc.
Used to be GSC, but they have been replaced by Black/White :P
Should have been made a poll.
I have to agree with Heath here. My favourite games have always been one were my completionist obsession can be somewhat maintained. When it gets crazy (400+ now isn't it?) my affection drops as I know deep down I can never get all the pokemon. Hell, I can't even get all the pokemon now; there's the bloody annoying "trade" evolutions which suck if you don't have anyone to trade with, and you can't trade on-line because you lose the pokemon. After that, there's the "promotion only" legendaries, which just ruin the game for me. Since when do I ever go to pokemon conventions or watch a film in Japan so I get some secret code? Never. It's just stupid and should be stopped. It's almost like on-disc DLC; it's there for you to obtain, if you go really out of your way to obtain it.
Rant over. For me, G/S/C. I always went for Silver though. I loved the whole "Two Regions" aspect. It drew me in.
The original Red/Blue! I have never spent so much time on any Pokemon game EVER! I usually have a tough time beating them now. As a kid I loved discovering the new Pokemon, and now I love all the fan-made art, music, creepy pastas, etc.
Without hesitation - The Second Generation. HeartGold and SilverSoul are two amazing games. I had to buy both to satisfy my needs.
I liked Hoenn, and Emerald is the last truly solid Pokémon game.
Tolerated Sinnoh, but no acceptance of the latest one.
I'm not sure why, but I feel like the pokemon designs have gone down somewhat from the beginning onwards.
There's one that is a chair or table or some smurfing thing now xD
Turtwig.
TURT - WIG.
Seriously.
Torterra is a pretty sweet name, though.