There are two kinds of racists:
1.) The blatant, hostile ones.
2.) The well-meaning one who nonetheless helps, willingly or unwillingly, to uphold the racial rules of our society.
We are, all of us, the second of the two, excepting only those few who are the first. Neo-Nazis, Klansmen, etc. The reason we are so averse to being called racist is because we as a society have delegated that word to meaning only the first of the two definitions.
Now how does that play into our depictions of racism? Well, look at any fantasy story since Tolkien. Look at the "races" there. Humans, orcs, elves, dwarves. All of them white (except the evil ones, of course, which tells you what else about race in Tolkien), and all of their "racism" depicted as being of the blatant, hostile variety. And since then, no Tolkien-ized fantasy world has had to deal with race in a nuanced manner.
The Walking Dead, as many people have pointed out, has handled race the most "cleanly." That is to say, not cleanly at all. That is to say, presenting it warts and all.
I'd also mention Rust, a game I haven't played but which has handled race in a refreshingly blunt and insightful way (as per this Extra Credits video):