Movie geek site Den of Geek has compiled a very interesting and informative list of the Top 50 movie special effects. 49 out of the 50 are accompanied by a Youtube-clip. 
For a rather average consumer like me, some of the choices are very interesting because they focus on things like colour-matching and lighting within the effect shot - things you would normally not even notice.
The list doesn´t focus on iconic SFX shots (no "Matrix"). To qualify, a shot had to be "either a) exceptionally convincing, b) ground-breaking or c) an exmeplary execution of an oft-used technique. Only one shot was allowed per film.".
At first 50 scenes seem rather plenty, but since even the earliest motion pictures made use of special effects there are many omissions which are up for discussion.
I think that early (French) cinema is a bit under exposed. "La voyage dans la lune" by Georges Méliès was made in 1902 and used split screens and stop-motion in the first ever science-fiction film.
I also think that the work of Jean Cocteau should have been included too. From "Le sang d´un poéte" (1930), "La belle et la bete" (1946) to "La Testament d´Orphee" (1960) he created the most astonishing worlds with simple, cheap and imaginative trickery. Even Hitchcock was so impressed that he asked Cocteau about his secrets.
Hitchcock himself is featured with two shots that I would not even have considered because they are so flawless that only specialists notice their influence. I would have gone for his more obvious, famous effects in "Vertigo" and "Rear Window" which probably explains why I didn´t do a list like this.
Of course there is also a Worst SFX list.
2009-01-02
Perfect Illusion
2008-11-16
"Let´s stay like this for a minute!"
This is the opening scene of "Rope". I wonder how this passed the production code of the era? Could "Hitch" have been any more obvious? The dialogue gets even better after this clip ends. "I wish we could have it done without the curtains closed, in the bright sunlight."
Besides being incredibly kinky and sexually repressed (like any Hitchcock film), "Rope" is memorable for another thing.
No, not the "one shot"-look.
It´s got one of the most fascinating film sets in history. When the constant bitching of the characters passes you by, you can still marvel at the ever changing, artificial skyline of New York City with it´s strange clouds drifting by.
2008-06-18
Rear Window

The spectre of Isadora Duncan and the reported cruelties the obsessed director inflicted on his willing victims resonate in this wonderful publicity shot of Tippie Hedren and Alfred Hitchcock by Lawrence Schiller.
2008-02-25
Pseudo Psycho
What to do, when you don´t have any original ideas but a big budget and a glossy magazine to fill? Why not copy and re-stage some famous film scenes? Scenes, so iconic and part of the shared unconsciusness of every 20th century movie-goer that its hard to fathom that they were all dreamed up by the same person: Alfred Hitchcock.
So Vanity Fair called up a bunch of famous actors who were certainly thankful for the free publicity, hired the creme de la creme of make-up artists, costume- and set designers...threw everything together and released it in their so-called "Hollywood Edition".
The finished photos are a strange mix of an overblown, failed attempt at camp, mis-casting and empty gloss. In other words: they´re incredibly funny!
The best idea and execution by a long shot is the "split screen" Psycho re-enacting with fresh Oscar winner Marion Cotillard as the showering corpse.
But things are quickly getting bizzare with Jodie Hedren as Tippie Foster in "The Birds"?
Seth Rogen as Cary Grant stand-in is nothing but a plane crash
Guess: Joan Crawford back from the dead? A doctored Glenn Close? Or Rene Zellweger after a long night? One could get Vertigo!
A "behind the scenes"-story, which explains some of the excesses of this production, can be found at Vanity Fair.
Watch the whole photo-spread here.