I think I am going to let nostalgia win this one and say Season One. Though it's not only
nostalgia because I feel it did have a strong overall story arc. And there's hardly an episode I don't like (I even like Bugs!). They were still finding their feet and even though some of the episodes were, um...full of plot holes, there was a lot of heart, great universe and character building and John Winchester!
Season Two and Three are close seconds. Season four was remarkably focussed and gave us a female character who had wonderful direction and purpose (though it's a hard one for me to re-watch because of the brother separation). Season Five was dark and painful (with some amazing episodes!), season six and seven were ok and I actually loved many of the episodes. Season eight has warmed on me. I really enjoyed the second half and I have a greater appreciation for the first half now.