Red/Blue/Yellow/Green~ Start of the Red and Blue Era, The Main character wins the championship.
Gold/Silver/Crystal~ Takes place after Red wins the Elite 4, Main character faces Red at the end of the game.
Ruby/Sapphire/Emerald~ Takes place after Diamond/Pearl , Gold/Silver/Crystal where the Main character takes down Team Magma/Aqua and wins the tittle.
Diamond/Pearl~ Takes place the same time Gold/Silver/Crystal Era, Because at the start of the game there's a TV Broadcast on a Red Gyarados at Lake Rage.
My proof is here in this link.
http://www.youtube.com/watch?v=Cb7UYGytAJMAny comments on the time timeline or suggestions?