Step One: Shape your character/creature/anyshit into an minecraft skin.
humans basic shaping:
eyes, mouth: darker skin color, hair. I don't put the mouth in my skins...
i'll won't go beyond, you'll need to learn at least this by yourselves.
Step Two: Shading your skin.
what i do:
first i select the color, example: blue, i want a dark blue. okay, i paint the dark area with this dark blue, then i select a lighter blue, and paint the surrounds of the darker one with it. keep going.
Step Three: Textures and other stuff.
you need to know that it's a bit different when you do some metal from when you do some cloath...i don't know a single s*it about this so let's skip.... and you'll need to know that an character will have stuff as bags, etc....for that, you make the part below of it more dark...

The only program i use is SkinEdit.
you didn't understood because of my english and cuz i'ma bad teacher?
Yeah, that's what's life's about mah friend... >.>