In chronological order, but not rank order, my favourites are Infiltrator, Downtime, Bereft, Targets, Terrors, Homefront, Alpha Male, Secrets, Misplaced, Coldhearted, Image and Agendas. And there are other episodes that I consider very strong too, of course!
I think my top 5 would be Downtime, Bereft, Coldhearted, Image and Agendas (again, in chronological order but not rank order). I loved the premises of those five episodes and the way they were handled. Seeing Atlantis in all its glory, having the Team wandering the desert with no memory of their time together, a snow day episode with beautiful visuals, great development for M'gann and the revelations surrounding her, seeing the whole League together on the Watchtower and Superboy finding out more about his origins etc.