For me its a tie between McCoy/McGann and Smith/Capaldi.
I really like the effect of the 7/8 transformation. The Frankenstein-esk lightning, the funny faces and the face smooshing and cracking to form the new look. And the way he used his post-regeneration super strength to bust open the door, and scouring the hospital halls with now idea of who he was. I liked it.
I also kind of like the unique circumstances of his death. Being introduced through NuWho, regeneration always had this big grand build up. But McCoy's death was extremely violent, and almost incidental. It may have not been the best swan song for McCoy, but it certainly made for an interesting regeneration.
I really liked 11/12, because it went through a lot of phases. First it was dire and desperate. Then loud and triumphant. Big and explosive. Then quiet. Sombre. Then melancholy and bitter-sweet, as 11 left us with his final words, putting on a brave optimistic face through the pain. He says goodbye, removes his bow-tie, and lets it happen.
Then for an instant Clara begs him to stay. But before he can even reassure her, SNAP. Capaldi. Surprise, mystery, suspense. Then a few jokes. The crash I didn't care for since if felt a little out of no-where and too similar to 10-11. But other than that, masterfully crafted and well paced.
I liked the jump cut to Capaldi. It was unexpected and different. All of NuWho regenerations have the same effect, while older ones all did it in their own unique way. I wouldn't mind if they tried some different stuff in the future.
Aside from that, the Night of the Doctor transformation was pretty cool too.