Episode: Season 3, Episode 2
What makes it killer: At this point in Season 3, we're just starting to find out who Miguel Prado is, and what he's capable of. The fact that he's grateful to Dexter for killing Freebo, and knows Dexter is a murderer, suggests that bigger things are in store for Miguel.
Additionally, it's the first time we see Dexter and Rita dealing with the revelation that she's pregnant. Including both of them making a hilarious pros and cons list.