I get a LOT of questions regarding what colors I use where when it comes to the ponies, and I keep saying I'm gonna make a little guide. Well, let's give it a shot.
For the majority of my covers, I use Copic markers to color. Copics are light-fast, alcohol markers... not unlike a classic school marker, but higher quality. I prefer Copic over other brands primarily for a few reasons: Variable tips (markers, fine, brush, etc), better blending, and they can be refilled! This is the BIG selling point to me... this means you can buy the marker once, and continue to refill. It also means you can custom blend colors should you desire. Copics also guarantee that if you buy Y00 yellow, and then buy another down the line, the colors will match. I've bought the same marker color from other brands and had them not match. I will use other brands here and there for very specific colors or effects, but Copic is 99% of my marker work.
So... when I do a cover or whatever, I do basic ink lines first with a Faber Castell PITT pen... a black sharpline pen with India ink. Basically I make a simple coloring book page. No mistakes allowed here... one can't effectively marker on top of white-out. Let it sit and cure about 30 minutes to avoid streaking and smearing. Also, use them carefully- do not do heavy hatching and blacks here, Then color, then do final full inks with brush and india ink. I can't put markers on top of my full, brushed inks- markers will smear it.
My choice of papers vary, but for the most part I use Strathmore 80 lb Recycled paper (400 series, green cover). For large pieces I use illustration board.
These are the BASIC colors I generally use for the basic pony palette. By NO MEANS am I saying these are the only choices or correct or whatever... use what looks good to you. I will say this, however- I strongly suggest working with paler colors first, then progressing to darker/bolder colors. You can always darken with markers, you can't really lighten. Watercolor theory.
Copics are designated by a letter and number system as well as a color name, but I'm going to give the letter/number here.
You'll also notice a lot of colors are shared among the girls. This is to match as close as I can to Hasbro's PMS Colors, as they share a lot of colors on the show, too. AJ's hair is same as Fluttershy's body, etc. You'll notice that cutie marks tend to match eye color, too (not a hard rule)
Main body: v01
Mane: B34 (I often use Prismacolor Brittany Blue here, not found a copic quite the same color)
Mane striping: V04 and RV06
Eyes- V04 at darkest with paler highlights , such as V01
Cutie Mark: RV06
Applejack- (also known as My Favorite of the mane 6
Main Body: Y35
Mane: Y00 (with R17 bands)
Eyes: yG06 with paler highlights such as YG01
Cutie Mark: R17 and YG06
Main: C0 (Rarity is NOT a white pony- she is GRAY. Pale, but gray. In contrast, Shining Armor is white. Observe her eyes against her coat)
Mane, top: BV13
Mane, under: V15
Eyes: B24 at darkest, fading to B01
Cutie Mark: B01
Main Body: Y00
Eyes: BG 45 at darkest, with paler highlights such as BG23
Cutie Mark: R00 (with BG45 butterfly body- it's so small for me I generally just make it black lines)
Main Body: R00
Cutie mark: B01 and Y00 (again, the balloon strings are so small, just black lines here... otherwise, same colors)
Eyes: B24 at darkest, fading to B01
Rainbow Dash... so many damn colors...
Main Body: B000
Mane: here we go... top to bottom, R17, Y38, Y00, YG06, B24, V15. Tail is same, just reversed direction.
Cutie Mark: R17, Y00, B24
Eyes: RV09 with paler highlights such as R23
Celestia- (again, NOT a white pony. Believe it or not, she's pink. But, extremely pale pink, so... )
Main Body: I leave her primarily white... but I take R000 and "trim" her edges, using it for pale shading to give her pink highlights... observe cover #5 to get an idea
mane: tricky... it fades out, so it's multiple colors. Generally, I use B00, YG11, BV00, and R00 for the pale areas, and darken as I go up by applying layers of the same colors to make it richer. At the top, I use darker versions or the same colors... generally B01 (I go as dark as b24), YG03, BV02, R10 (or as dark as R23)
Cutie Mark: Y00, Y11, y35
Eyes: RV06 at darkest, fading to R10
Armor: Base color of Y00, and golden shading as appropriate... I sometimes go into oranges or browns, but I also like Y26 and Y28. Don't forget her V04 stones!
Luna ( also known as Best pony overall!)
Mane body: B95
mane: B24 (sometimes I use B18) with B00 highlights (on the show, her mane is a diaphanous fog... it's clear at the edges. I draw it more as hair... easier on me!)
Cutie Mark: Black
Eyes: BG49 fading to BG 23
Armor: B01 trim on black
main Body: V12 (Just a tiny bit off from Twilight)
Crest and Dorsal spines: VG06
Belly plates: VG11
Head fins: Vg01
Eyes: VG06 fading to VG01
All the crew have orange(!) tongues, I use YR 15, and R39 for mouth interior.
Derpy, Vinyl, Chrysalis, yada yada yada will have to come at another date, but this is our Starring cast. Again, notice that a majority of colors repeat... gives them a unified palette and this is pretty accurate to the show guidelines in my guidebook. Also makes it easier to block in same colors at same time
Copics are available at Hobby Lobby and Michael's, some colors you may have to order as they carry limited range. But, play with 'em... takes some getting used to. Remember to keep them wet, dryer markers equal more streaking and blotching (not bad for effects, lousy for smooth coverage.)
As always with the ponies... HAVE FUN DAMMIT.