I think the timeline of the games goes like this.
Red/Blue/Green/Yellow/FireRed/LeafGreen & Ruby/Sapphire/Emerald.
Gold/Silver/Crystal/HeartGold/SoulSilver & Diamond/Pearl/Platinum.
Black/White.
Black 2/White 2.
X/Y.
The other games which I think are canon though I don't where they are placed in the timeline are Colosseum, XD: Gale of Darkness, Battle Revolution, Ranger, Ranger: Shadows of Almia and Ranger: Guardian Signs and I guess Snap could be, there's no reason it couldn't be.
The games that I think are not canon and are in another universe are the Mystery Dungeon series, PokePark series, Rumble series and Conquest as that is a crossover game with Japan only franchise Nobunaga's Ambition which features characters from the Dynasty Warriors, Samurai Chronicles and Warriors Orochi franchises.
I know there are other games but I don't feel like getting into those right now.