Yellow > Blue > Red
Silver > Gold > Crystal
Ruby > Sapphire > Emerald
Diamond > Pearl > Platinum
SoulSilver > HeartGold
Black > White
Black 2 > White
X > Y
Alpha Sapphire > Omega Ruby
Sun > Moon
Ultra Sun > Ultra Moon
I couldn't find anything about FireRed and LeafGreen.
I already stated in a comment that this Reddit thread says that the third versions never sold more than the other versions combined. This, however, doesn't necessarily mean that the third version was not less popular. For a third version to be more popular than one of the other versions, it would have had to sell more than half as many units as the other versions combined. (except for the case of R/B/G, as there were three versions.) Because Crystal did not sell more than half as many units as Gold and Silver, it is not possible for it to be more popular than both. The same applies for both Emerald and Platinum. Just wanted to throw that out there.
Blue is listed at 5.03 million copies, while Red is only 4.83 million. Interestingly enough, Yellow beat them both at 5.10. I had heard Gen 1 sales were closer to the 30 million mark though, so this data is most likely a bit outdated.
I'm not sure if these numbers included Virtual Console sales.
Silver sold 3.85 million, Gold sold 3.75 million.
Once again, not sure if these numbers included Virtual Console sales.
Ruby sold 2.84 million, Sapphire sold 2.76 million.
This Bulbapedia article claims that Ruby sold more than Sapphire.
This Bulbapedia article claims that Diamond sold more than Pearl in the US by the end of April 2007. The sales charts for Japan in that article also indicate that, by the end of the eighth week of their release, Diamond had sold ~400,000 more units than Pearl.
[...] with the SoulSilver version selling 1.01 million and HeartGold selling 0.76 million units.
As of September 2010, Black sold 1,323,000 copies, while White only sold 1,234,000.
Pokémon Black 2 and White 2 sold 1,561,738 units on their first week on the Japanese market, being 816,576 from Pokémon Black 2 and 745,162 from Pokémon White 2.
Black 2 sold ~71,000 more copies than White 2 in the first week in Japan. Obviously, White 2 could have sold more copies than Black 2 by now.
Pokémon X and Y sold 1,866,570 units on their first week on the Japanese market, being 961,003 from Pokémon X and 905,567 from Pokémon Y.
This is only for the first week and, on top of that X only sold ~55,000 more copies than Y. It's likely that Y could have sold more copies than X by now, however, based on what I've seen, X is the more popular of the two. X being more popular than Y is also backed up in the Reddit thread linked below.
Pokémon Omega Ruby and Alpha Sapphire sold 1,508,665 units on their first week on the Japanese market, being approximately 614,000 from Pokémon Omega Ruby, 714,000 from Pokémon Alpha Sapphire, and 180,994 from the Double Pack.
Once again, those sales numbers are only for the first week of their release in Japan, but Alpha Sapphire sold ~100,000 more copies than Omega Ruby. Based on from what I know, I think Alpha Sapphire is the more popular of the two.
Pokémon Sun and Moon sold 1,893,387 units on their first week on the Japanese market, being approximately 808,000 from Pokémon Sun, 783,000 from Pokémon Moon, and 302,758 from the Double Pack.
Obviously, the difference in sales between the two is ~25,000, which really isn't that big. It's not unlikely that Moon has sold more copies than Sun by now.
Pokémon Ultra Sun and Ultra Moon hold a rating of 84.43% and 82.96%, respectively, on GameRankings.
Haven't found any separate sales numbers stating how much each game has sold yet, but GameRankings rated Ultra Sun nearly 1.5% higher than Ultra Moon. This could indicate that Ultra Sun is more popular than Ultra Moon, but it doesn't at all mean that Ultra Sun has sold more copies than Ultra Moon. However, I feel that Moon is more popular than Sun and Ultra Moon is more popular than Ultra Sun, based on what I've seen online.
Everything in blockquotes is fromthis Reddit thread unless stated otherwise. Also, I'm not sure if the sales listed there are wolrdwide sales or just for one country.