okay before i start off remember this is not the only way to make pixels. This is how i make them so you can read it and learn from it apply what you like to your own art.
i would put this on my art blog but seeing this is to celebrate me hitting 3000 followers on my main im gonna put this there
the program I use to make pixels is Adobe Photoshop Elements 9
here is a finish product of the pixel I used in this tutorial
if you have any questions feel free to ask