As you know, for a 3d picture, you have to take 2 images both of which will represent the views of both your eyes. But that doesn't mean you take 1 image via the viewfinder of your left eye, and the other via the viewfinder of your right eye. The result will have too much difference in them.
Instead take multiple pictures, starting from the left eye point of view (the 'master' or first picture from which a 3d picture will be made), and then slowly moving the camera towards the right taking successive snapshots. Notice the motion should be very slow. The slower the motion and the more number of snapshots in between, better are the chances of you getting the perfect picture.
Now you have to assemble the picture using a program called 'plascolin', you may also use gimp for the purpose.
Open the left image first in plascolin, then it's automatically going to open the next image in the same folder in alphabetic order and combine them so as to form the 3d image.
Now for the perfect picture.
You've taken multiple images, if the difference between the selected left and right image is too much, viewing the picture will be a headache, if it's too less, the 3d effect wont be much. Ideally, ½ inch difference between the left and right images will be the best, but still it's not guaranteed to be the best; from here our quest begins for the perfect 3d image.
So in the list of images, first make multiple folders; in these folders you'll pair 2 images, the first one being the left most image in all cases; i.e. in all these folders, there will be a symlink (or copy) to the first image.
Now you have to select the second image, start off by symlinking the rightmost image to the first folder. Make a 3d image off these 2 images, if you find that you're getting headaches (if you're not, you've found the perfect picture), move the 4th or 5th rightmost image to the second folder, check the results, if you find there're no headaches, move the 3rd or 4th rightmost image to another folder, but if you do have headaches with the 4th or 5th image also, proceed to the 7th or 8th image. Preview both to see what's best and continue doing the same until you find your perfect image.
I hope you understand what I mean. You've to find the image which 'just' wont give you the headaches, that'll give you the best 3d effect.
Now for a sample --
This's my 13 year old dog. Notice the hair, they really look nice.