Season 2 certainly had some pivotal episodes, which interestingly, seemed to be grouped together, in the main. But I think that Season 1 stands out, not only because it establishes the parameters of this world, that in fact, shares more commonalities with our own than one might be led to believe, but also because I found, that there was often a blend of strangeness, mystery, and otherworldliness (not talking about the literal kind here) that pervaded a number of episodes. I suppose I'm thinking here about the presentation of production elements more than specific plots or storylines. There was an odd, almost alchemical quality to the merging of key lighting, musical cues that had a peculiar and ineluctable quality, spare dialogue at times, and a simple evocation of the unknown, that made the greatest impression on me. For all the scorn heaped on it, I think of The Alternative Factor in this way, as well as, Charlie X, WNMHGB, Enemy Within, LIttle Girls, Miri, Dagger of the Mind, The Menagerie, and Return of the Archons, in this light, as well as a number of others.
So for me, I think the distinguishing factor that was most impressive was the different sense of presence or atmosphere, rather than, of necessity, the stories or characters, that forged a unique identity for the show.