Wargs. Merry and Pippin on Treebeard. Shots in Kazadum. Numerous riding shots that were reshoots. The entire dinosaur stampede in Kong. I could go on.
I will say this. The Fellowship of the Ring Extended, out of all the new trilogy films that have been out recently, is the best. It's a masterpiece.
I will not comment on Kong.
The Rings Trilogy is more inconsistent but again, I personally see that in all of Weta's work aside from the main visual effect (ie, Kong or Gollum).