Twilight Sparkle:
Body: Lavender
Hair: Royal AKA Midnight Blue, Fuchsia, and Purple
Other: Navy may also work for the blue in Twi's hair, but it could be a bit too dark. As for the purple in her hair, you may be able to substitute Violet or Jewel. Fuchsia is really the best option for the pink.

Pinkie Pie:
Body: Paris Pink or (Bubblegum Pink)
Hair: Fuchsia

Fluttershy:
Body: Yellow
Hair: Bubblegum Pink or (Blush)
Other: Do not be tempted to buy Baby Pink minky - although it may look like a good fluttershy pink, it is extremely light... Literally almost white.

Applejack:
Body: Mango
Hair: Yellow or (Ivory?)
Other: There really is no comparison to the Mango minky, which is why I haven't listed an alternative color. Orange is too dark, Sunshine is too yellow... So if you see mango, and you're planning on making an Applejack in the future, buy it before the store runs out! Also, I don't have a swatch for the ivory minky, but from what I can see in pictures, it seems like it could possibly be a good alternative to yellow for her hair.

Rarity:
Body: White or (Snow White)
Hair: Purple
Other: White and Snow White are basically the same exact color.

Rainbow Dash:
Body: Baby Blue or (Sky)
Hair: Cherry, Orange, Yellow, Dark Lime, Azure, and Purple
Other: Although Baby Blue is ever so slightly too light for Rainbow Dash, Sky is a bit too dark. And unfortunately there is no in-between color. You'll just have to choose which one you like better - slightly light or slightly dark.

Princess Celestia:
Body: White or (Snow White)
Hair: Bubblegum Pink, Sage, Sky, and Violet
Other: The colors in Celestia's hair are slightly dull - the minky shades recommended above will help achieve those slightly dull colors. If you want to go more vibrant, however, you may want to use Paris Pink, Dark Lime, Azure, and Jewel.

Princess Luna:
Body: Royal AKA Midnight Blue or (Navy, suggested by *Sophillia)
Hair: Electric Blue
Other: To help achieve the transparent look of Luna's hair (in season 2), you can use a transparent fabric such as organza or tulle layered over the electric blue minky.
Helpful Tip: ~munchforlunch suggests that if you want to buy fabric from only one place (to reduce shipping costs), you can use Electric Blue for the body, sparkling organza layered over electric blue for the hair, and Baby Blue for the hooves.

Apple Bloom:
Body: Yellow
Hair: Cherry

Sweetie Belle:
Body: White or (Snow White)
Hair: Violet or (Jewel) and Bubblegum Pink

Scootaloo:
Body: Orange
Hair: Raspberry or (Fuchsia)

Derpy
Body: Grey or (Silver)
Hair: Yellow
Other: Some people like to use Dusty Blue for Derpy - as you can tell from the name, it has more blue tones than the grey or silver minky.

Dr. Whooves:
Body: Cappuccino
Hair: Mocha or (Dark Brown)
Other: I'd recommend ordering swatches of the browns, just in case, because they can be difficult to photograph and see their true colors.

Big Macintosh:
Body: Cherry
Hair: Orange

Octavia:
Body: Silver
Hair: Charcoal
Other: If you want to go darker than Charcoal for the mane, the next darkest shade is Black.

Bon Bon:
Body: Yellow
Hair: Royal AKA Midnight Blue and Paris Pink

Spitfire:
Body: Canary AKA Bright Yellow
Hair: Sunshine and Orange
Wonderbolts Uniform/Costume: Electric Blue and Canary AKA Bright Yellow

Soarin':
Body: Baby Blue
Hair: Royal AKA Midnight Blue
Wonderbolts Uniform/Costume: Electric Blue and Canary AKA Bright Yellow

Vinyl Scratch:
Body: White or (Snow White)
Hair: Turquoise and Electric Blue

Granny Smith:
Body: Dark Lime or (Opal, if you want a more muted green)
Hair: Yellow

Lyra:
Body: Opal or (Tiffany)
Hair: Baby Blue and White
Other: For Lyra's mane, you can choose from a couple blues... As alternatives for Baby Blue, Aqua and Tiffany could be good choices.

Daring Do:
Body:Camel
Hair: Black, Charcoal, Grey, and Ivory
Clothing: Olive and Jade
Other: Hunter would be a great color for her clothing, along with Olive, but I can't find it in stock anywhere! So Jade + Olive will have to work. (I know Jade looks super, super bright in the picture, but trust me on this: it's not even half as bright in real life! The picture is not accurate at all.)

Cheerilee:
Body: Raspberry
Hair: Bubblegum Pink and Blush

The Great and Powerful Trixie:
Body: Sky or (Cobalt)
Hair: Baby Blue and White
Other: Trixie is a true cornflower blue, and unfortunately, there are no minky colors that match her perfectly. Sky is more cornflower than any, but is a few shades too light. I know some other plushie makers have had success with Cobalt, although it is a few shades too dark - so you'll just have to choose if you want slightly light or slightly dark for her body!

Thank you ~munchforlunch, ~thetypeofpony, ~Tawny0wl, *Sophillia and *NerdyMind for contributing to the list!