I didn't like the 3D with Thor much because the glasses make the films darker. It doesn't seem like they take this into account much with regard to turning up the brightness, so it just feels like I'm watching a movie with sunglasses on the entire time. It also doesn't help that I already wear glasses, so the 3D glasses fit rather awkwardly around them.
I didn't notice any beneficial 3D scenes in Thor though. I've mentioned it before, but the best example of 3D that I've seen in the theater was actually a little demo reel for RealD 3D with this ball that floated "off" of the screen and out toward you. Most 3D only seems like a pop-up book to me... things are only slightly off-set compared to the stuff in the background, and they don't always use it to reflect movement between the background and the foreground (the foreground being the area created by the 3D effect).
They also really need to stop trying to use 3D to make it look like something is coming right at you. I believe the latest Resident Evil: Afterlife movie did this with the fight scene in the shower room (the axe being thrown), and the problem with it is that you aren't fully immersed because of being able to easily see the edges of the screen. In that way, the object is usually cut off before it looks like it will actually reach you.