Well, if you are talking really brilliantly-made works of cinematic genius, I would submit practically the entire Hitchcock oeuvre.
An early favorite of mine is Murnau's Nosferatu: The Symphony of Horror. I have seen about 1000 different versions of the same footage (b&w, tinted, colorized, no soundtrack, organ soundtrack, live sountrack, etc.). It still remains one of the best-composed horror movies out there.
Another vastly underrated classic was Ridley Scott's ALIEN. When it came out it was unfairly derided as "HALLOWEEN-in-space"; what it really represented was a conscious re-imagining of the tropes and motifs of post-victorian Gothic literature. It took all the recurring themes - a crumbling castle, implied rape, the dangers of playing god - and modernized them. A very smart movie... it always bothered me that people didn't realize what the movie was trying to accomplish.
And, yes, I did write a 20+ page term paper on the subject in my first year of grad school
To be honest, I didn't realize how carefully-constructed the set of symbols in ALIEN was until I started the research for the paper.
But, as far as timeless, favorite movies - I still have to say JAWS and EMPIRE STRIKES BACK (man, I like dark movies!). It's nice to see that I'm not alone on that one.
