New and improved! EDIT: Rainbow's yellow mane/cutie mark color was incorrectly listed. This has since been fixed, please redownload the updated copy.
All of the color guides are getting a revamp. The guides are all now two pages, one for digital applications (such as vectors, painting in Photoshop, 3D modeling, etc) and the other for print applications (customs, merch, T-shirts, et cetera). The PNG preview for the digital guide should be OK to use as well, so the PDF is optional.
If you use Google Chrome or Safari, they will attempt to open the file in-line with Google Docs PDF viewer. DO NOT EYEDROP THOSE COLORS. SAVE THE PDF FILE. The Google Docs viewer displays in a very low bit depth that results in dithering of the colors. Until Deviantart gives me a way to disable this, you should use the download file link to view the guide!
They are also now more space efficient, and will be able to scale better with ponies that have more colors than normal.
The Digital guides aim to be as close to the show as possible, while the print guides aim to be as close to official merch as possible. When there's no merch of that pony (e.g. background ponies) then the print colors will be based on my conversions which will aim to reproduce the show without looking too weird or have obvious gamut problems.
It is safe to eyedrop the digital colors or use the hex/RGB codes - the swatches should match up just fine. Just make sure you're working in sRGB color mode.
For the merch guides, the spot colors are rendered using CMYK alternate color space. This is based on my own examinations of the merch boxes, where the spot colors are simulated straight to process anyway.