That truly was difficult. If I had to choose from the options above, it would have to be Angelus. For reasons stated by others, but he was just so ruthless and cruel. The height of his cruelty was how he set up Jenny's body in "Passion". As if killing her wasn't enough, he wanted Giles to experience the epitome of pain by setting his house up so that it seemed like Jenny had a special night planned. From the roses, to the champagne, right down to the music...it was just too much. The moment Giles discovered Jenny's body, I literally had to close my eyes and cover my ears with my hands. It was just too much to handle, and for that, Angelus will probably always win by a long shot.
But I picked Angelus only because I think you overlooked another Big Bad: themselves. As I have stated before, season 6 is my favorite season. The trials and tribulations they went through in season 6 hit closer to home than any other arc on the show for me, especially Buffy's arc. I don't know what it's like to come back from heaven, but I do know a thing or two about having your previously happy existence being ripped apart, and you're stuck in this existential "dead end", this zombie like state, where you would do anything "just to feel". As Dark Willow was only the result of Tara's death, the entire arc of season 6 dealt with the Scoobies being at their absolute worst. Life was the Big Bad, and I connected to that more than anything else.