Here is a great tutorial on how to make 3D pics.
Before we start there are a few things you are going to need:
1. Any old digital camera. Anything will do, i used my iPhone 4
2. A computer program. Its called StereoPhoto Maker. It super lite weight, it doesn't even require you to install it. You can download it for windows here
3. Something that allows your computer to read SD cards.
Optionally you will need a tripod for your camera, or a table. I dont have a tripod so i used a table. If you think you have very very steady hands, then you may be able to do it without.
Ok lets get started. A 3DS image is 2 different jpegs images that have been merged together, so what we need to do is take two images, that are very similar to each other but at slightly different angles.
Step 1.
Get your 3D image set up ready so your images can be taken. My set up looked like this, since i used a table. I took my photos resting my iPhone on the higher table to take a picture of my 3DS.

Step 2.
Once your set up has been complete, you need to take two images. Both very similar, but at slightly different angles. One image angled a bit to the left, one a bit to the right. The images should be almost identical apart from the change in angle, on the same level, no change in up and down angle etc.. images i took wernt perfectly on the same level, because i didnt have a tripod. But my image looks great on my 3DS. Here are the images i took.
Image angled slightly to the right

Image angled slightly to the left

Step 3.
Next you need to put the images on the computer, so do that. And then load up that program you downloaded.
Step 4.
You will see a screen like this. I have marked the icon you will need to click with a red circle:

On clicking this icon, you will be told to open a left eye image, and after that you will be asked to open a right eye image.
This is important Your left eye image must be the image that is angled to the right, and your right eye image must be the image that is angled to the left. So that if you looked at both images, the angles kinda 'cross over' if that makes any sense at all. After selecting you images you will see a screen like this:

Step 5.
If you have got this far, your almost done. From here go to 'File' and then press 'Save MPO file..'
How you name the file is important as it is how the images are detected by the 3DS. There are many ways to name them, id recommend you name you images something like '3DS_0001' without the speech marks. that number part at the end must be above (0000). Here's an example of mine:

Step 6.
You now have your 3D image for your 3DS. Take your SD card out of your 3DS and put it in the computer. Look for the folder in that SD card that says 'DCIM' then go to the next folder, which will contain all your pictures. Drag the new .mpo file you just made into the folder that contains the pictures.
Step 7.
Your done! Stick the SD card back in your 3DS, load up the photo channel thing and view your photos. If you did all the steps right, you can now see a 3D photo on your 3DS. Be aware, if the file size of this picture is large, it will take longer to load your 3D image.