Older movies that are actually filmed in 3D give the biggest effect. Black Lagoon is superb and feels natural, House of Wax with Vincent Price as well. About the only older movie in 3D that I didn't much care for was Jaws 3-D. The effects are actually quite good, but they are almost TOO in your face. It may be the only movie to give me a headache, and I'm not sure if that was the case or if the film grain is so heavy that it actually gets in the way of viewing the movie properly.
Thing is, most movies that are causing the issue these days are ones that are NOT filmed in 3D...and because the cinematographer is not trying to capture a 3D image at the time, it makes editing it into a 3D movie a nightmare of bad depth (or almost so natural the depth is not noticeable), element stretching or bending (Clash of the Titans 3D is a big example of this...good night, was that terrible conversion), or hurtful on the eyes due to the editing. If you watch Hugo, you'll notice a lot of Hugo is sweeping, long-take shots, with lots of follows and pans. It does not cut away to different shots as often as regularly-shot movies, because Scorsese was aware that 3D has to be accomplished a certain way. When you do post-conversion, none of that is taken into account, thus why more people don't like it; it gives them headaches because it was not edited or filmed in a way that benefits the technology.
So, I agree that post-conversion 3D doesn't give much benefit, and usually non-3D movies converted to 3D suffer from "$3 extra" ticket-price syndrome and nothing else. But there are plenty of newer 3D movies that look right, too. Even if they are horror movies...and granted, not all that great...the last two Final Destination movies do have very solid 3D cinematography (especially 5, if you can believe that), and even if I'm not really a fan of the series, I do appreciate it when somebody does the process right. Fright Night 3D was OK, but unfortunately, the movie is too dark to really appreciate any effect you get from it.