To preface, I have to say that I only use MSpaint to do my pixels. Some people use fancy programs specifically designed for pixelling and others use photoshop. I did my first pixel piece on MSpaint, and that is what I use to this day. However, I do use photoshop to make transparent backgrounds.
Number One: Pick a palette!
First and foremost, you need to pick a palette. You can tweak it along as you go and you may very well change the entire thing, however it is always good to start off with the basic colors of your piece.
For this piece I chose two, simple five-color palettes. You never want to use MSpaint‘s default colors. Always use your own custom colors.
Number Two: Shading
There are two basic types of shading when it comes to pixel art: dithering and cel shading. Some artists strictly use one or the other while others combine the two.
Dithering is accomplished by placing individual pixels o the next proceeding color at a set rate along the edge of your previous color.
Dithering is best used for a more “realistic” piece.
Cel shading uses midtones to blend two colors together. This is accomplished either by placing a 1px line completely down the division or in strategic places along the division. If you followed my advice in step one and picked a good palette, this method shouldn’t be a problem.
Number Three: Outlines
Okay, so you now have your palette and you know which type of shading you want to use. Now you need to know which outline format you want to use: isometric or non-isometric. 
Isometric pixel art is any object that has defined angles and rules you abide by so that it is shown in a 3/4 view (or a variety of other angles, but this is most common.
Non-isometric is any other type of pixel art that does not follow the rules of angles and as such allows for much more artistic freedom.
Technique:
Now that we have covered the basics, it’s now time to create your pixel art! I have had many people ask me how they can become better at pixelling and the only thing I can say it practice! I am amazed at how far I have come just in the past year of pixelling. I have learned from trial and error.
I prefer solely to work in non-isometric form. This is simply personal preference. I started out working with a lot of dithering, but I have found that I enjoy cel shading much more. I like the “cartoony” feel you can achieve with cel shading that you often cannot when using dithering as a shading tool.
I always start with simple outlines. You never want your outlines to be all one color though. They should be the darkest shade of whatever color you are outlining. Follow this up with a quick color fill in each section so you can get a general feel for the piece. After that, start your shading. I like working from dark to light as I find it easier.
I feel it is now time to mention that a large part of pixelling is the fact that you are tricking the human eye into seeing what the brain wants to. What I mean is, small gaps in a line can appear smoother and make your piece less jagged. This is why it is so important to pick the right color palette. If you don’t, you won’t be able to trick the eye into seeing what you want it to.
Trial and error is the best way to figure this out. However, if you have photoshop you have the ability to “cheat” using layers and opacity to find the perfect midtone between two colors.
Good luck and happy pixelling!
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