Various programs are quite good for skin-making. I personally use paint.NET (not a website), you probably have heard of it at some point. I've heard some use GIMP, some use MCSkin3D developed by PMC user Paril, and a few others. However, almost all programs are fine as long as the skin is not an obvious copy of anything else.
Well, after playing Team Fortress 2, I decided to play some Minecraft (with mods). I had a rocket launcher. Then I thought: "What about rocket jumps in Minecraft?". I aimed the rocket under my feet, I shot, and I exploded.