Seasons 1 and 2 areeasilythe best. Season 3 was just plain boring and it didn't feel like Dexter, and season 4 was very good, but no match for the shear epic scope of the plots in season 1 and 2. When your first season deals with the true identity of the protagonist and the fate of a forgotten brother, and your second season deals with Dexter's kills being found and the manhunt for him, there really is no contest. It's hard to live up to that in the following seasons.
I just watched all 4 seasons for the first time in the space of 2 weeks, and my order of favourites goes like this: 2, 1, 4, 3.