Most of these sales are from the first few weeks and months of the games, and spread either over America, Japan, or all countries. (Europe, America and Japan.)
Gen 1
In the United States, Pokémon Red has sold 4.83 million copies, while Pokémon Blue has sold 5.02 million copies.
This is from a Bulbapedia article for Red and Blue.
Pokemon Blue > Red
Gen 2
I can't remember where I found the source but Silver sold more than Gold. I attempted to hunt down the source but I can't find it.
Gen 3
Ruby sold more than Sapphire, too many sources to count.
Gen 4
By the end of April 2007, the US release of Pokémon Diamond had sold approximately 1.045 million copies, and Pokémon Pearl had sold approximately 712 thousand copies.
Bulbapedia's article about the games.
So, Pearl < Diamond.
Gen 5
The tracking firm lists total Black & White sales at 2,558,000 units. Black was the better selling of the two, at 1,323,000 units. White sold 1,234,000 units.
I checked a few sources but this one had the best reliability. It is from andriasang.com
Who couldn't like Reshiram? What a cool guy!
Anyways, Black sold more than white.
Gen 6
Again, forgot the source and it's vanished, but X sold more.
