The theme, the design/layout, the encounter design/variety.
IMO my all time favourite raid is Naxxramas. One overriding theme (scourge), the introduction of the "wing" design with five separate wings with their own theme (in keeping with the main theme), the final wing only being accessible after the last boss of the first four wings is defeated. It was a great raid, the only thing that comes close for me is Kara (which ironically follows none of that methodology lol).