I try to separate machines that have similar shots / layouts. For example, fan layouts, upper right flipper, etc...
I also make sure 2 widebody machines aren't next to each other since I have pingulps.
And if there is a high traffic area or tight space, I'll put a machine with a launch button vs. a launch or plunger that sticks out.
I also keep kid friendly games near each other and away from adult themed or more challenging games.