Well here's the way I've calculated it.
The Beginning - Pokemon FireRed and LeafGreen - Pokemon Ruby, Sapphire and Emerald & Pokemon Colosseum are all set in the same time period. My reasoning behind this is the fact that during mission in which the player has to help Celio get the transfer machine working he refers to Hoenn in the current tense which implies the games are set at the same time whereas in Colosseum their is a transfer machine that works in similar manor and during the timing of that game no Gen IV pokemon were discovered or even known.
Later Years - Pokemon HG/SS/Pt/D/P/Pt & Pokemon XD Gale of Darkness
Gold and Silver as everyone knows was set 3 years after FireRed and LeafGreen which naturally makes it later in the timeline and numerous references are made in the game to "Mt Moon Square, Professor Elm and the 2 Legendary Mascots" which as we know Mt Moon Square didn't exist until some point in between FR & LG which seems to imply that both games take places in the same timeline or atleast a very close one. Pokemon XD Gale of Darkness is set 5 years after Colosseum and the presents of Munchlax and Bonsly seem to imply the timelines are rather close to that of D/P/PT.
Further in the future - Pokemon Black and White
The main evidence which bases itself on this games timing is the fact that Cynthia references her battle to Lucas and Giratina which took place in the events of Pokemon Platinum which of course suggests it was in the past.
Now - Pokemon Black and White 2
Clearly set ahead of Pokemon BW as even the title of the game suggests swell as the countless time it's mentioned in the game.
So as far as I see it it goes like this.
Pokemon FireRed/LeafGreen & Pokemon Emerald, Ruby and Sapphire are all set at the start of the series.
Pokemon Colosseum and Pokemon XD Gale of Darkness are set sometime during or between these events.
Pokemon HeartGold/SoulSilver/Platinum/Diamond & Pearl are all set (at least) 3 years following the events of FireRed and Leaf Green
Pokemon Black and White is set after the events of Pokemon Platinum
Pokemon Black 2 and White 2 are set ahead of the events of Pokemon Black and White.
Friend Code: 4742-7095-3187
Current Team: Charizard Y, Chesnaught, Greninja, Tyrantrum & egg