For a lot of the orcs, it was really good make up. For the head orc in the first movie, he had to sit in the make up chair for 11 hours.
There was a computer program designed for the LOTR movies called "massive" where they can take shots of crowds and duplicate them in different ways so they all look different. They also created the CG flame program for the balrog.
Helms deep was both CG and live action.
Hope this helps.