A step by step for those who are interested. There are probably better methods to do everything I do and of course wayyy better artists... But if you are interested in my process then here it is XD
Original Picture on DA: http://miss-cats.deviantart.com/art/Discord-x-Fluttershy-Day-24-578893332
Original Picture on FA: http://www.furaffinity.net/view/18565059/

I hope my explanations are clear..

1. Just the lineart. I started with a sketch and cleaned it up, this was the result.
2. I made a new layer underneath and put a basic color to fill in the lineart.
3. I transparency locked the layer and colored in the base colors and background color.
4. I made a adjustment layer for Photo Filter on the sepia color to adjust the colors a bit to fit the background, I turned it into a clipping mask over the base colors so it wouldn't interfere with the background color.
5. I created a new layer above the base colors, set it to multiply, lowered the layer opacity, made it a clipping mask to the base colors layer, and tested a few colors out until I had a color I was satisfied with for the shading color. I believe it was a lightish red color that I settled with.
6. I made another layer, also a clipping mask, set it to screen and tested out a few colors until I was satisfied with a lighting color. I made another after that and set to overlay and colored over the highlights to brighten it up and give it a more yellow tone.
7. I merged all the layers together and started coloring over the lineart and certain areas, cleaning up the entire pic. This is where I really get in there and work out the details and make it look much cleaner. This is also where I really regret adding wings to the drawing. This part also takes the longest.
8. I made a multiply layer over my main layer set as a clipping mask. I put some darker areas in where I think it would be darkest, to make it look more 3d.
9. I take the sponge tool set on saturate 13% and I go over the edges of the lighting parts, the part where the lighted area meets the midtone area. I also take a brush with the hardness on 0% and with a low opacity i go over the edges of the picture where the light hits, to give a almost glowy effect.
10. I used "Lens Correction" in the filter list to make the dark edges ( could also just do it with a brush but meh ). I made the lighting used a brush for dusty rain stuff falling. I drew in some butterflies, copied them and put the copied layer on "hard light". I then used a airbrush on low hardness and opacity over the butterflies for the glowy-ness.