I'm working on an article about deleted scenes that were subsequently restored in director's cut or special editions of films - but that weren't in the original theatrical edition. I'm not talking about DVD extras, I mean scenes that were actually reincorporated into the movie.
Perhaps two of the best examples I can think of to demonstrate what I'm talking about are the "French plantation" scene from Apocalypse Now and the "Gobi Desert" scene from Close Encounters. Both scenes were missing in the original theatrical release, but are now (at least in some circles) considered to be classic scenes.
I'm looking for more examples along those lines. (Other films which keep cropping up in my research are LOTR, Aliens, Blade Runner.)