Here, I'm going to compare the Gold and Silver versions to give you the basic idea of which is the better one. I'll start with noting the differences.
In Gold, you can catch different pokémon than in Silver. In Silver, the levels of Ho-oh and Lugia are different from Gold. Then Gold has different graphics than Silver.
Different pokémon
In Gold, you can catch Mankey, Sandshrew, Teddiursa, Spinarak, Mantine and Gligar. In Silver, you can catch Vulpix, Meowth, Skarmory, Ledyba, Delibird and Phanpy. Primeape, Persian, Ursaring, Ariados, Mantine, Gligar, Ledian and Delibird are hardly ever used, leaving one useful pokémon in Gold and three useful pokémon in Silver. Silver: 1 - Gold:0
Ho-oh and Lugia
You all know in Silver, Lugia is level 40 and Ho-oh is level 70, and in Gold, it's the other way around, right? Well, you should also know that the level 40 Gold Ho-oh is better than the level 70 Silver one, and the level 40 Silver Lugia is better than the level 70 Gold one because at level 70, they've forgotten their best moves.
Now, let's think about it. A Ho-oh with Sacred fire is great, but a Ho-oh with Fire blast is not that bad. A little worse, but it's okay.
On the other hand, a Lugia with Aeroblast is great, but a Lugia with Hydro pump is useless. I mean, how CAN Lugia be stupid enough to forget the best Flying attack for the second best Water attack? The average damage for Hydro pump is less than the average damage for Surf because of the accuracy. I haven't seen a single Lugia in a serious team with Hydro pump. And Lugia gets STAB for Aeroblast, but not for Hydro pump. If you also count the high Critical hit ratio for Aeroblast, you'll find out that Aeroblast is about two times better than Hydro pump on Lugia. For short, Lugia is just plain stupid with Hydro pump compared to Aeroblast.
So, Gold gets a great Ho-oh and a terrible Lugia, and Silver gets an okay Ho-oh and a great Lugia. Figure out by yourself where this round's point goes. Silver: 2 - Gold: 0
Graphics
I think the Gold ones are better. When I first saw the Silver pokémon sprites, they somehow all appeared upside-down. Some of the Silver sprites are much better than the Gold ones, though. And I think the Yellow graphics are the best out of all the games - if you count out the fact that the colors are not good, of course. But my opinion that the Gold graphics are better might just be because my version is Gold. I don't really know wether I should put the point to Gold or just don't count this part, but either way, Silver wins.
So, I hope you enjoyed this section.