I do quite a bit of 3d photography. I use a sputnik 6x6 medium format stereo TLR, as well as an old realist 3d half-frame 35mm.
I've found that range to subject is critical. With cameras that have lenses approximately the same distance as the human eye, the 3d effect is best when the closest object is 5-15 feet away from the camera. Farther then that, you end up with a flat image, closer and it becomes straining to view.
When taking photos of large items further then 15 feet away (like a building), you will get a better 3d effect if you increase the distance between the lenses. I do this by putting a cap on one lens, taking the photo and then moving slightly to the left, switching the caps, and taking the 2nd photo.
There's a 1/30th rule in stereo photography that states that for the best 3d effect the subject distance should be 30 times the distance between lenses. So, if your taking a photo of a building 300 feet away, the lenses should be 10 feet apart. If you're taking a photo of the moon the lenses should be 7000 miles apart (this has been done and the 3d effect is fantastic! it makes the moon look like a little ball floating a few feet in front of you).
It's also important to understand convergence--the images should converge at the point of interest, and it's best if this is the closet object in the scene.
Here's a good resource:
Stereoscopic photography with a single camera