Well, the only real difference between Gold/Silver is the Pokémon that are missing from each version.
In Gold, you will have to trade for Ekans/Arbok, Vulpix/Ninetales, Meowth/Persian, Ledyba/Ledian, Phanpy/Donphan, Delibird, and Skarmory.
In Silver, you will need to trade for Sandshrew/Sandslash, Growlithe/Arcanine, Mankey/Primeape, Spinarak/Ariados, Teddiursa/Ursaring, Mantine, and Gligar.
In Crystal, you will need to trade for Vulpix/Ninetales, Mankey/Primeape, Mareep/Flaaffy/Ampharos, Girafarig, and Remoraid/Octillery.
In Gold/Silver/Crystal, you will need to trade with Red/Blue/Yellow for Bulbasaur/Ivysaur/Venusaur, Charmander/Charmeleon/Charizard, Squirtle/Wartortle/Blastoise, Omanyte/Omastar, Kabuto/Kabutops, Articuno, Zapdos, Moltres, Mewtwo, and Mew.
Crystal has a lot more features than G/S/C did, so out of Gold/Silver/Crystal, I would play Crystal. However, between Gold and Silver, it is basically just a matter of personal preference, which set of exclusive Pokémon you like better.
