Darla's pregnancy arc was great. It raised so many interesting questions about vampire lore, and about what it means to have a soul or not. It was also a complete game changer for pretty much every character on the show. Even though Angel says he never could have loved Darla while he was soulless, I thought this arc still did a good job acknowledging the fact that these two traipsed around the world together for something like 150 years. 150 years! No matter what, those two would always be connected. Darla also had one of the most memorable and poignant (second) deaths in the entire Buffyverse. The downside is that this storyline ran concurrent with Angel's obsession with W&H, which became tiresome after a few episodes.
Second is the Angelus arc. It comes in second only because I think there was a bit of a wasted opportunity there. Angelus is such a significant villain in the Buffyverse, and ever since BTVS S2, everyone was basically waiting for the day when he would make a comeback. I think they just didn't push the envelope enough when he finally reappeared. Like, I sort of wish they had had the guts to have him kill a member of the Fang Gang or something. I dunno. Something super dramatic. Overall it was still good though. I just think, with Angelus, there is always the opportunity to have your biggest shock value moments, and I just didn't think that was the case on his ATS arc. I also like this arc because it brought Faith back into the mix, better than I ever remembered her.