April 24 update: New version added with improved fit for the 4/4S and a taper feature to allow you to taper the walls of your case, improving grip. Also opening up all iphone size variables for tweaks. A number of smaller improvements are also included.

March 16 Update: Couple of changes in this version:
Integrated the code from Makerbot's geometric customizable cases here, so you can choose what type of case to generate.
Further tweaks on the phone sizing - should now fit better on iPhone 5

The first step is Benjamin's Stencil Factory chaaawa.com/stencil_factory. - detailed instructions are below.

Once you have the output of Stencil Factory ready, open this thing in Customizer and copy the output of Stencil Factory into the "Input" field.

Next, use the customizer parameters to select the correct phone model (iPhone 4/4s vs. iPhone 5), the case thickness, and any scale / position changes you want for your image.

Click save to STL and you're ready to print!

Note: The case tolerance field should only be adjusted if you've already printed and need to make fine adjustments.

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The following instructions are copied directly from Benjamin's Stencil-o-Matic:

Pic.1 Open the Stencil Factory and select your image (gif, png, jpg).
"Convert & copy", as its name suggests, also copies the output in your clipboard, so:
Pic.2 "Open in Customizer" and paste in "input".
Pic.3 "create STL", download and print.

Stencil Factory also available in .zip (with sources) for offline use.