Sorry for the lack of photos, some got deleted by accident. I hope my descriptions and your imagination will suffice! :) )

Having a custom made mobile cover made can be quite expensive, and if you don't mind being creative and draw something yourself, this can be done very cheap!

I bought two very cheap very thin mobile covers on ebay for just a buck each. Search for your phone model, followed by 'ultra thin cover' and see if there is anything like the one I used.
Prices can vary depending on your phone, and some covers are matte and others are shiny. See if you can find something with a matte/rough surface both inside and outside the cover.

Step 1: You Will Need:

A cover, fitting your phone (duh!). Can be found on ebay. It HAS to be transparent, and I recommend clear white, unless you don't mind a coloured tint.
A sketch of your motive. You can either draw one yourself, or print it out. Make sure it has the same size as the cover.
A sharpie
Colour pencils or coloured sharpies. Pencils works best if the cover is matte inside, but if it wont stick, use sharpies or even paint.
Some kind of flexible varnish. If the cover is flexible, the varnish also need to be, otherwise it will crack.

Step 2: Make an Outline

Again, sorry for the lack of pictures.. I actually had one for this step, but now its gone :(

First thing first: The motive needs to be made INSIDE the cover! This is why its very important that the cover is transparent. If this is not possible to find, I will get to that part later.
The reason for this, is because a phone usually gets a lot of abrasion when being pulled up and down pant pockets. Making the motive on the outside, most likely wouldn't hold for very long.

Draw or print your motive, and make sure it fits the size of the cover. You can do this by tracing the outline of the cover on a piece of paper (remember to mark things like camera whole and other stuff, so you know where they are so the motive can be placed just right according to it). Cut it out, and draw your image.

Tape the image on the outside of the cover, so you can see the sketch though the cover. Trace it with a sharpie on the inside.

Step 3: Colour In!

Now its time to colour your motive!

I highly recommend using colour pencils, since they are the easiest to work with. However, if the surface is too smooth they might not stick. This is why its a good idea to find a cover with a rough/matte surface, but unfortunately that can be pretty hard to know if you order it online (being matte on the outside doesn't mean its also matte on the inside. I ordered two covers in different colours from the same seller, and only one of them was also matte on the inside, and the other was smooth).

You can also colour with sharpies if it will stick better :)

Or you can even use paint, but this is really tricky since you need to work 'backwards' in a sense. Usually when painting, you add colour, shadow, details and the like on top of each paint layer, but this has to be viewed from the opposite side, so you need to paint all the details and shadows first.

By my experience colour pencils is the easiest to blend and work details and shadows, even though it has to be viewed from the opposite site.

Step 4: Varnish

Once you are satisfied by how it looks from the outside of the cover, you need to protect it.

This can be done with varnish, preferably something flexible like decoupage or acrylic lacquer. If the cover is very flexible too, the varnish needs to be able to follow the flexibility without cracking.
Paint the varnish on your motive on the inside of the cover, and let it dry. Give it a few layers if necessary.

When I made this cover the first time I made it on the outside of the cover (discovering that it wore off within just a few days) and I also used spray varnish, which wasn't very flexible at all. It didn't take long before the varnish got a few loose edges, and I could pull off the entire varnish, drawing and everything!

Step 5: Alternatives, If the Cover Isn't Transparent

When I first discovered how easy this was, I ordered a cover for everyone in my family and made them some personal christmas gifts. However, I couldn't find a transparent cover for my boyfriends phone and ended up with a solid black hard plastic cover. So I had to figure out something else!

It was a good thing the cover was hard and less flexible (for except its really difficult to remove from the phone, but thats another issue...) otherwise I don't think this would have worked.

I decided to paint it with acrylics paint, however I know from experience that plastic paint on smooth plastic surfaces usually don't hold. It would just be a matter of time before it would wear ends so you could just peel it off, if it won't fall off by itself eventually.

Toilet paper and super glue

To make a better surface, I glued one layer of toilet paper on the cover. It can be messy and a bit tricky, so you need to be careful not to screw it up, and end up with bubly or torn paper.
I added a few super glue drops at the time, and quickly evened it out with an old piece of credit card, cut to a manageable size. Don't glue the whole cover before adding the paper, otherwise it will just dry before you're done with the other areas.
Make sure all the paper has absorbed the glue and sticks to the surface.
This gives a very unique and rough surface, ready to paint once its dry.
Remember to finish it all up with some varnish. At this point, its less important how flexible it is, as long as it is at least as flexible as the cover itself.

This can most likely only be done if the cover is very hard. I did the same thing with my other cover, that was too smooth to colour on the inside with pencils, but too flexible to hold super glued toilet paper - it just fell off.

Embroidery

But what if its not hard plastic? What if its silicone or rubber?
Some sharpies work just fine on the outside of rubber/silicone, so you can just draw your motive how you like it. Maybe use a white board marker to make a sketch directly on the cover.

Or, you can do something else - make an embroidery. It doesn't really take much skill (I never tried it before until I made these gifts, and I found an extra for my mom that was just plain white silicone).
Make a sketch with a white board marker, thread a needle and begin sewing! Be careful not to mess up the string when you pull it through (put a finger in the loop on the inside of the cover, so to carefully guide the string through the whole without making a knot).
Some material can be hard, and you might want to use some tools to poke through it with the needle, and pull it out.
Some material is the opposite, and might be a little too soft - be careful not to poke too many wholes in the same area.

Be creative! Fool around and try whatever :)