Gen 1 - Pokemon Fire Red/ Leaf Green
These are much easier to find then Yellow on the gameboy, plus they have extra islands to visit, after beating the elite 4.
Gen 2 - Pokemon Heart Gold/ Soul Silver
They have the added stuff from Crystal, plus they are more likely to work, since the gameboy colour gold/silver/crystal internal battery have probably run out, and no longer save data.
Gen 3 - Pokemon Emerald
Most likely Alpha Sapphire and Omega Ruby will have added stuff from Emerald, but this is the ultimate version for this gen at the moment.
Gen 4 - Pokemon Platinum
Gen $ - Pokemon Black and White/Black 2 and White 2
These are the odd ones out, as there is no 3rd version, but if you pick Black and Black 2, then you will be able to get both version legendaries, the same would happen if you pick White and White 2.
Gen 6 - Pokemon X and Y
No 3rd version announced at the moment.