The events from Red, Green, Blue, Yellow, FireRed, LeafGreen, Ruby, Sapphire, Emerald, AlphaRuby and OmegaSapphire happen first.

Then, 3 years later, the events from Gold, Silver, Crystal, HeartGold, SoulSilver, Diamond, Pearl, and Platinum happen.

Some years after those (it's unknown how much time exactly), the events from Black and White happen.

2 years after that, the events from Black 2, White 2, X and Y happen.

As it's not mentioned in a timeline of handheld games, I always imagined that Pokemon Colosseum and its sequel happened in some sort of Pokemon post-apocalypse.