Actually, there are multiple lines of pokémon-safe cosmetics for this purpose. You can thank the popularity of contests and performances for both, but suffice to say, painting or putting makeup on your pokémon is actually more common of an occurrence than you’d think.
That having been said, I don’t exactly have first-hand experience with any particular brand, but supposedly, Sweet Pecha is the one that many of the topmost coordinators swear by. According to the editor of this blog, anyway. If you’re into more of a punk/goth line, Rash Bash is also fairly popular, especially when it comes to pokémon dyes.