Looking at your sprites, they appear to be handdrawn in a basic graphics program like MS Paint. Correct?
Great! That is ideal for drawing up a ship, giving it color and even giving it some depth and detail.
From there you could add further detail, color, shading and depth in an advanced graphics program such as Photoshop, Corel Draw or (completely free) Gimp.
How do you add depth in a simple program such as MS Paint, so that it doesn't look as flat, you ask? Simple. Pick a color, create a simple pallete for it, ranging from very dark to very light. Then add the darkest shade of the color on the outer edges of your ship, and then work inward, making it lighter and ligher. Eventually, your ship will appear to have some depth.
This can then be improved upon and augmented in an advanced graphics program, allowing you to add differences in lighting, shading, etc.
Here you can see an example from one of my Antediluvian sprites:
1.) The lower part has already received some detail and depth in paint, the top half hasn't. As a result it looks very flat. Right next to the ship you can see two simple color palettes. Copying the colors and adding them around the edges of the ship will result in giving it a less flat, more 3D look.
2.) The ship has received detail and depth in MS Paint.
3.) The colors have received some augmentation in an advanced graphics program. The contrast has been improved.
4.) The ship has received darker shadows around the outer edges and brighter lighting on the center, resulting in more depth and an overall more interesting look.