Cuts:
Too many individual edits to list, but these are the main ones:
All unnecessary characters were axed - Rita, Astor, Cody and Paul are the major ones.
All unnecessary sub-plots, not tied to the Ice Truck Killer storyline were hacked: All but three of Dexter's kills-of-the-week, Bautista's marriage, the murder of the police officer, the politics between LaGuerta and the Captain, Dexter trying to help Jeremy Downs, Dexter's biological father and the inheritance.
All non-essential plot lines tied to the Ice Truck Killer storyline were chopped: the security guard as the first suspect, the kid in the trunk who might identify Dexter and Neil Perry confessing to being the Ice Truck Killer.
Many flashbacks that did not add to the overall story were severed.
To eliminate the bookending/episodic feel of a TV show, nearly all of Dexter's intro/outros to each episode were slashed.
Finally, the reveal of the Ice Truck Killer's identity is delayed to the point that the audience is now on the same page as the characters on screen.