This website/program is free to use and actually models the skin for you whilst you make it, so you can see how it will look, without needing to upload it or download a Skin Viewer. It also gives you a collection of presets to use as well as a decent colour chart, and if you know what colour you want, you can just type in the hex code of that colour and it will have it there for you, I used it when I first started making skins and it is a great beginner program!
http://adf.ly/7RrHn Other than that the most obvious choice would be Photoshop, which is what I use. It isn't as difficult to use as you, probably, think it is and it gives you more choices and customisation options than that site. The only problem would be the price, but I'm sure you could easily get it free with a bit of searching around!
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(Sorry for the
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