1, 2, 4, 5, 3. I think in the end, season 6 will sort of be a tie with 4 in terms of "best seasons".
3 is damn near a throwaway season if you ask me. I'm sort of irked at the concept of them simply bringing up a rival serial killer in every season, but the whole Trinity Killer with Lithgow brought my faith back in that. Dude murdered that role. I liked season 5, because it brought the romance dynamic back into the picture- and that season it was real... unlike with Rita, because he hid half his life from her. I think Julia Styles did a good job in her role. The end of the season was what was disappointing though, and I think left people not happy with it.
Much credit to Michael C. Hall for going through cancer treatments and a divorce, yet still producing/starring in this show along side his now ex-wife.