I'll probably never be a big Hitchcock fan, sadly. I think I had just heard too much about his work or seen his ideas referenced too much by other directors, so by the time I got to his stuff, it didn't have the punch and immediacy that it has for a lot of other people. He seems like a director who was profoundly disinterested in character except insofar as it might be employed to further the plot. I'm really character-centric, so that's a problem for me. Also, he usually seems to really call attention to some of his visionary shooting/framing. It comes off as ostentatious and showy, and pulls me out of the story. Or there's story elements that I can't suspend my disbelief long enough to appreciate. Even if Strangers on A Train was a literal re-telling of actual events I couldn't believe it. Cops shooting into a carousel full of children?? I don't think I would have bought that even in the fifties. And luring a man out into the middle of nowhere where he's all by himself, and then sending a plane after him, as opposed to just sending agents in a car to pick him up (posing as the guy he's supposed to contact) and then treating him like Abe Vigoda in the Godfather?. I love North by Northwest, but I just have to pretend that that scene didn't happen as soon as it's over, and then just imagine he'd been on the wrong street so the bad guys couldn't pick him up. The rest of the film is quite enjoyable though. Anyway....
Vertigo's probably my all time favorite; hardly surprising given that it's really a character study and not much else. Stewart is magnetic (definitely my favorite performance of his), and Barbara Bel Geddes is smoldering and commanding every second she's on screen, and I remember being a trifle irritated every time the story veered away from her and back to Novak. Also, the camera trickery didn't seem as obtrusive as it does in some films (that one shot in Notorious where the camera moves in from the corner of the room to the key in Cary Grant's hand yanks me inexorably from the film every time I see it). The cameras seemed to be serving the story in this film, to great effect. Finally, the characters' motivations are sensibly realized, whereas most of the time Hitchcock doesn't seem interested in letting us see why the characters do what they do (I remember once complaing to my brother, who is both older and wiser "So just how exactly does Ingrid Bergman fall in love with Cary Grant in the space of about five minutes? I've never seen that happen in real life." To which my brother dryly replied, "Well, you're no Cary Grant."). The only performance I really really like in Notorious is the bad guy husband (Claude Rains? I can't even remember).
In second place, would be Hitchcock's Rope. Most Hitchcock fans tend to push this aside as more of a technical exercise than a movie that tells a story. For me, most Hitchcock films come across more as technical exercises than anything else, so I don't see why that should be more the case for Rope than large chunks of his other movies. Still there's just an energy and flow to this film that really keeps me thoroughly engrossed in the story. It feels like you're watching a play, and everything just keeps moving forward. Hitchcock does something really great here, he puts himself in a position where he can't do a lot of his much-lauded "look at me, no one's ever thought to frame a shot like this before, white girls!!" shots, so he really forced himself into a corner where the actors have to do the heavy lifting. And when he does let the camera hold sway, it's in an understated and masterful way (like the shot from the dining room into the kitchen through the swinging door, where we see the murderer gleefully holding the murder weapon aloft above a kitchen drawer. The door then swings shut, then swings back open as we see the villain, now empty-handed, smugly closing the kitchen drawer. The door swings shut again. To my mind, that's an example of the camera really giving you insight into character. The guy is so smug and self-satisfied with himself that getting away with it would never be enough of a charge for him. He needs an audience to see how good he is, to understand that he could have gotten away with it, even though they were dining on the coffin. He's a killer, but it's really only an extension of his narcisism. Everything -- the performances, the camera moves, the plot, is economical, tight, and lean. Sure, maybe the movie was marketed on the gimmick of the one camera/no cuts thing, but this film feels like less of a technical exercise to me than any other Hitchcock film I've ever seen. Oh, I also love the cut-out skyline in the background. What a frigging great movie. I imagine if Hitchcock hadn't been constrained by the gimmick, I wouldn't like the film nearly as much.
Third place would almost certainly go to Lifeboat, another Hitchcock film that probably could have been a play, and definitely benefits enormously from the severe constraints in terms of set and camera positions, if I had never seen The Lady Vanishes. Again the protagonists are in a confined environment, and the film is very tightly plotted. Also, the performances seem to just breathe better than in a lot of Hitchcock's films, the tension between the male and female leads seems less forced and more natural (who have the typical love/hate romance thing going on), and the characters don't just come off as plot engines. I don't want to say too much about this one just in case some people here haven't seen it yet, as it's not as well known as some of his films (not like it's a secret or anything, but whatever).
Sorry this is so long.