Season Three by a mile. It was the only year I truly enjoyed the show. The opening arc switching between realities was the high point of the series, and the second half was almost as good.
S1-2 was just chock full of standalone episodes I did not care at all for. There were only a handful of good episodes. I actually stopped watching mid-way through S2.
Season Four was, enh. I really REALLY did not like the fact that the continuity rebooted, we weren't with the same characters anymore, and the mirror universe was gone.
Season Five wasn't very good either. I commend them for moving into a Observer-ruled future, BUT every episode was just about going after some Macguffin and I just didn't care.