#2. Use it to Bring Details to Life
3D doesn't have to just be for huge obvious depth differences like hands coming out at you or deep landscapes going into the screen. If you are doing the film in proper 3D (see point #4 above) it's precise enough to show even little differences, like bumps on tweed or weathered wood, which they did in Up.
You probably didn't consciously notice that Karl's jacket was bumpy and you didn't go telling your friends, "That cracked wood was coming right at me!" but subconsciously, it makes tweed feel tweedier and makes old boards feel worn, the same way people and things feel older when photographed with high contrast lighting.
Without you knowing it, those textures do more to draw you into the scene than any big, sweeping spectacle could. When everything in Karl's house is slightly tweedy and worn, it really adds to making it feel like the house of an old man that time has passed by, without any of it standing out and catching your attention. It's that same musty feeling you get when visiting grandma, except you can leave.
#1. Use it to Help Tell the Story
I'm sure we can all imagine how 3D could undermine a good story by adding a bunch of cheesy distractions ("3D Citizen Kane" is pretty much the catchphrase of anyone arguing against 3D) but if the technology's not being wielded by a ham-fisted spastic, it can also be used to help tell the story.
Ham-fisted spastic on the set of Dungeon Siege.
For instance, every movie you've ever seen has used the camera to help you feel something in a scene. You usually don't notice it (that's the idea) but every good film maker uses camera angles, lighting and color to help draw you in. Horror movies tend to be the least subtle; the angle and lighting on a face can make the killer look scarier:
Though the right casting helps
So for a director who knows how to use it, 3D can be another tool that plays the same kind of subconscious tricks on an audience.
For instance, normally the twin 3D cameras are placed about the same distance apart as the average person's eyes. But if the director changes that distance in a scene, it can immediately give you a sense of disorientation. If you saw Coraline in 3D, you saw a great example of this; they used that trick in the creepy spiraling tunnel that led to Coraline's weird-ass alternate world.
Watching that scene gives you the subconscious feeling that something is wrong, something you just can't put your finger on. For people who hate subtlety, they make it pretty obvious what's wrong later on.
It can also be used to up the tension; for instance in a 2D film, a heavy rain just partially obscures the scene. But when shot in 3D you subconsciously find yourself trying to squint and peer past the raindrops. That feeling of depth in the shot makes you instinctively want to work to see what's behind the obstruction. It engages you, and draws you into the shot to try to make out the monster, or psychopath, or naked woman standing back there. You'll squint and dart your eyes around and maybe even move your head.
But that's just the beginning; the most interesting uses of 3D are the ones great film makers will be coming up with 10 or 20 years from now, once the tool has been in the hands of dozens of creative minds, innovating across multiple films. Meanwhile, bad film makers will still be using it to make shit jump out of the screen.
That's really the point; when you boil it all down, 3D is just one more tool for a film maker to use, for better or worse, just as same knife can be used to carve a beautiful sculpture or stab a stranger in the dick. At the end of the day the invention of 3D is no different than the invention of color film.
To this day, movies don't have to have color to be great...
...but once given the tool, great film makers make amazing use of it.
3D will be no different. Sometimes, you may even get that rare gem that uses both.
Now playing in theaters nationwide, please go see it