There are some pretty good harmonies on Pet Sounds. I can't really think of any Beatles songs where they are harmonizing with different vocal parts - which is what stands out to me from Pet Sounds - but I'm sure there are some.
Crosby, Stills and Nash (with or without Young) have some great harmonies. Their harmonies have always stood out to me.
http://www.youtube.com/watch?v=1-S6md3LNgs