Definitely season 1 for me, I thought the Dexter being chased bit was too cliched and also too early, we've only had 12 episodes to meet Dexter and he's already under the gun and being chased by the police?
The first season had it all, more killings, the other serial killer, Dexter's own side investigations and the little games they played, and then the finale was incredible, Dexter killing his brother was the moment of drama television of 2008 for me. It was even better than that, it was one of the best episodes of anything I've seen.
Second season was good, but it didn't have enough twists really, other than Lila killing Doakes. I knew Dexter would escape somehow because there's no way he wouldn't, whereas in the first season it was a puzzle slowly being solved, mystery meets crime meets thriller meets action etc. The way it unravelled, and the fact that finding out who the ice truck killer was minor in comparison with finding out he was Dexter's brother, was just amazing.
Season 1 was easily the best for me.