Ok, I had this finished last summer, but school happened. The method is very hard to understand in writing, so I'll try to upload some pictures soon to make it comprehensible.
Here is the Tofurkeymeister approved Ub3r-1337 method for custom skymaps outlined in 10 simple steps.
1. Grab an SLR camera (preferably) and head to an open field with as little obstructions on the horizon as possible.
2. Keep the lens zoomed at an optimal setting, enough so there is little distortion but not too far zoomed that you have to take 9001 pictures.
3. Look at the horizon and lock the exposure, you don't want the sun screwing up your pictures.
4. Shoot 10 pictures in a vertical line, from the horizon to directly overhead, with each picture overlapping slightly (You will look like an idiot while doing so

).
5. Return your camera to the horizon, shift so that the new pictures overlapping the old slightly (20%), and repeat until 360 degrees is established.
6. Upload the pictures to your computer. You should have around 150-200 photos, roughly. Run autostitch (
AutoStitch)
7.Under options set the scale to 10% (Else you run out of memory :O ), JPEG quality to 100, and memory to the highest amount, preferably 2 GB. Set SIFT scale to 25%. Load pictures, and RENDER

.
8. If memory runs out, lower JPEG quality/image scale. You can also up the image size, though don't count on it. If the image doesn't stitch nicely, try setting the SIFT scale to 50% or something else.
9. Open up the result in GIMP or Photoshop. Remove the foliage/buildings on the horizon using cloning/whatever other method you want. Add a solid color to the bottom of the image so that the fog of the map can match. (
The few bottom lines must be the same color, otherwise you get striping in the editor) Also, make sure the bottom few lines and the area above it blend, as the editor will take the bottom lines and extend that color down to directly below the map. Do the same to the top if needed, to prevent the horrible stretching effect which
sometimes occurs.
10.1 Resize the image to 2048 by XXX (Preferably 512).
10.2 Export as a .dds file
GIMP:
GIMP DDS plugin
Photoshop:
NVIDIA Plug-ins for Adobe Photoshop (Normal/Cube Maps, DDS)
10.3 Load the .dds in your map like any other skytexture.
P.S. The later stages of the method work on textures from CGTextures.com as well.