In my not-at-all-humble opinion:
1.) Gold/Silver/Crystal. As stated above, these games are the best Pokemon generation ever. The only games that look like they could even contend for this #1 spot are Diamond and Pearl...and even then, they don't have 16 gym badges to collect. Gold/Silver/Crystal = Pure Ownage.
2.) FireRed/LeafGreen. Remakes of the original greatness that started this all. Because they add so much new content (Vs. Seeker is love) on top of the original fantastic quest, they get the #2 spot instead of the originals.
3.) Red/Blue/Yellow. Ah, the games that started my love affair with Pokemon. How could I ever forget you? While you will always have a place in my heart...your offspring just did things better. Well, with the exception of #4.
4.) Ruby/Sapphire/Emerald. I'll just say it, I really didn't care for these games at all. After the flawless G/S/C games, this was just a slap in my face. You take away all the time based events and replace them with...a Pokemon fashion contest. Great (feel the sarcasm dripping from that word). Oh, and now we have natures, which just makes catching Pokemon with decent stats a royal pain in my posterior. Yes, I liked some of the new Hoenn Pokemon. No, this didn't make up for the rest of the game being a shell of the previous generation.
Thankfully the future of Pokemon looks bright. Diamond and Pearl seem like they will either be the best of the series, or at least second place, when they are released next week. So exciting...