The physical appearance isn't so important really...these days, they can make anyone look like anyone with enough prosthetics and CGI. I always sort of imagined the Judge as a huge fat baby...soft, pale and bald like a eunuch...but with a hawkish intelligence and savage wit. Not to mention a terrifying grin.
Malkovich can certainly be creepy and scary, and as long as the script is strong, the intelligence should come across...he can play evil genius.
Since my original post, I haven't really spent much time thinking about who would be the ideal cast...so I'm coming up with alternatives off the top of my head here: I could also see Larry Drake as a great Judge, though he may be a bit old now. Hell, maybe even Matt Lucas if he could cover up his British accent...he certainly fits the bill physically.
Hard to come up with someone to play the Kid since we hardly learn anything about him in the book. I'm thinking someone slight and dark like Anton Yelchin or even Zac Efron (these two picks based purely on physical appearance)...but we'll probably get Shia LaBeouf.
EDIT: Maybe Joseph Gordon Levitt for the Kid?