Since some people are having difficulties with the custom paintjobs, here's a short pictorial tutorial for you all. ;)
This tutorial was done in Adobe Photoshop Elements 1. Different versions of Photoshop will have slightly different tools, and more advanced Photoshops will have tools that you can play with to further enhance your images. Elements doesn't have any of the frills that other versions have, but it works fine. Paint Shop Pro would probably work too, though the method would have to be different, and I don't have or use PSP, so I can't elaborate on that.
Start by opening up your template in Photoshop. Your template guitar should have all the individual components set as seperate layers (body, bridge, pickups etc - don't worry about the strings). To do this, simply use the freehand lasso tool to draw around the components, then copy and paste them onto new layers.
Like so:

In the above picture, I have desaturated the body colour from red to grey to give me a more neutral colour to overlay pictures onto. To do that, select the layer with the body, and simply use the desaturate tool in freehand (the icon resembles a sponge).
After that, get the picture you want to overlay onto the guitar, and copy and paste it onto your template.


Play around with the picture for a bit until it's in the position you want it to be. When you've done that, select the layer which has the body of the guitar (that's the ONLY thing that should be on that layer) and find the magic wand tool. Click somewhere on the background of the image (NOT on the guitar) and you should end up with something like this:

Now, navigate back to the layer with your overlayed image (careful not to deselect the area you've just selected) and press 'Delete'. If all has gone well, it should look like this:

Right, nearly done then. To finish off, simply fiddle about with the layer type until satisfied. 'Overlay' normally gives good results (as seen in the picture below), but there's no right or wrong type to choose, just pick whichever one you like the best.

After that, simply repeat the process again for the headstock. Depending on how detailed your original template is, you may or may not lose the headstock logo when you overlay an image. The template I'm using was procured from tschommer from this very forum after my own template was lost in a tragic accident that destoyed 3 years worth of data. Ask nicely and someone might send you their template if you need one. ;)
In true Blue Peter tradition, here's one I made earlier (with the same source image) so you can see what a properly finished one looks like (though I make no claim to professionalism - some of the others on this forum are far better):

That's not the most scientific of tutorials, and you can mess about for a fair bit beyond what I've covered so far. There have been guys doing inlays and fretboard mods too, which I haven't tried (yet!) and haven't attempted to cover here, so if anyone wants to add their own tutorials onto this thread, please do so. The same goes for anyone who wants to correct anything I may have typed wrongly.
So, there you go, now go hunt down some pictures and get photoshopping! :D