Gold/Silver is best. Gen II is always best gen. But that said I've played all the games (at least one from each generation) and they all have their ups and downs.
Gen I had a lot of glitches and I was too young when I first played it to fully appreciate the art of team-building and battling. I only ever started to take things beyond type-matching when I started playing Silver.
Gen III is REALLY underrated, gets a lot of hate, and is one of my favorite gens despite all of that. I'll never understand why people hate it so much. I know the water routes were annoying and there weren't any oldies in there and all, and maybe it was a bit short/easy to complete, but it was a great gen. The graphics in R/S/E were my favorite of all the games as well.
Gen IV is my least favorite. The story is okay but it's nothing captivating, and none of the IV pokemon really captured my attention.
Gen V was great, and Black and White 2 was pretty good also. Rocking storyline. I think mostly everyone loves N.
I have a lot of feelings about Pokemon.
Yeah I agree, Emerald was my all time favorite and still is, but after trying out heartgold they both have pretty much been my favorites....BUT I STILL LOVE EMERALD!!!!