I think that Season 3 has been the best season so far.
It feels very much like the show at its peak. With all the world and character building done to such a degree that we knew where we were and who lived there, the season had a sturdy foundation to tell stories on. The result is a sequence of episodes operating on optimum, each one smartly utilizing the promise of what the previous seasons laid out:
You had some of the best, Rusty is a bastard super scientist episodes (The Doctor is Sin, The Buddy System)
Stripped of his right to arch, you had some of the best of Monarch's attempts to mess with Rusty anyway (Home is Where the Hate Is, Tears of a Sea Cow)