I think season 2's my favorite. It had Minefield about Lt. Reed facing his mortality while Archer was trying to save his life. It had The Communicator, where people had to do a covert mission. In The Crossing, people's bodies were taken over, and there was a brief period when this was a mystery. In Horizon, Mayweather dealt with his father's death and tried to come to terms with his own family. Cogenitor dealt with the rights of oppressed people. First Flight had guest actors doing a great job as pilots. And Bounty had Archer deal with being kidnapped, and debate with a Tellarite.