All of them! My personal favorite is the Johto arc, G/S/C. Crystal kind of comes in half-way so they bake Silver+Gold+Crystal arcs together into one, as I see it.
But if you don't want to read them in order and just want one really cool, you should get the Ruby&Sapphire arc. Ruby's and Saph's missions and stories are different from the earlier arcs, the plot and episodes they face are both emotional and action-packed, the gym leaders and Steven are featured a lot and are important in the plot, especially Norman and Wallace I guess, so there are a lot of interesting characters playing around in the arc. And it's epic, the ending should leave you crying or panting or laughing and yeah, overall it's just a really great arc. I happen to love the Johto characters and the region, but I have to admit that as a standalone arc in Pokémon Special, Ruby&Sapphire might be better.
